there really isn't a very clearly articulated early example of a mechanical plot device in a major RPG, not before the mid-80's anyway (Toon comes to mind, and I think Gangster! maybe had some such elements, both games were published sometime in the mid-80's to my recollection). I think you can certainly argue that Traveller, by eliminating the whole 'character progression' element of play from the mechanics, was TRYING to turn the focus towards RP (You can only advance your character in terms of the fictional narrative, though some of those improvements will translate back to mechanical advantages in terms of better ships, guns, armor, etc).
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there were also, a bit later, games like 'Skyrealms of Jorune' which were very emphatic about stories and settings being the central focus. These could be seen as incipient story games (even EPT falls into this category, as its setting is really its big thing, the rules are basically just variant OD&D with a few customizations). NONE of them, AFAIK (not a Jorune guru) has actual mechanics or play procedure that give players any sort of dramatic input outside of their characters actual choices in-game.
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but the essential mechanics [of Traveller] are still D&D-esque in the sense that they fall to the rules to resolve conflict and the player's input is through character choices and actions modulated by the mechanics of skills etc. IN THEORY you might move to the level of a PC using EDU to basically say "Yeah, I know about this type of animal, as a xenobiologist I should know about its reproductive strategy", but that would be followed by a dice roll against 'xenobiology' (and note that even EDU doesn't play a defined role here, though you might get a modifier to the skill check). There's no mechanic for "I invoke my EDU to make up lore about the creature's reproductive strategy that we can use to help us find a way to eradicate it" or something like that. Not even Social Standing has that, although it could be argued to be fairly strongly implied within the stock Imperium setting that the game basically assumes. Still, there isn't a way to even make a check against an ability score directly, the GM would have to just decide for himself if it would work, or else break it down into a detailed process that would involve existing skills.
Well, I'm a great believer in the possibility of what Ron Edwards calls "vanilla narrativism" - that is, "story now" RPGing without player-side mechanics to support it beyond the sorts of action declarations one gets in classic D&D, Rolemaster, etc.
So I think that you can have player-driven, story-focused RPGing without the sort of metagame mechanics you describe. But you need to use procedures that are different from the Gygaxian GM-as-dictator. Taking suggestions is probably the most important. These can be suggestions from the players about world elements (places, NPCs, etc) that need to be settled for the game to go ahead, and that are relevant to their PCs backstories, goals etc; and also suggestions about where the game is going to go next.
With your example of xenobiology, the player can ask "Can we stop it by toying with its reproductive strategy?" And if the GM takes the suggestion, then that means "say 'yes' or roll the dice" - assuming it's an important issue in play (those dame tribbles!) then the GM will call for a roll. If the roll succeeds, the strategy works.
In the context of Traveller, this depends (I think) on taking the lead of the books in setting appropriate difficulties for throws, and allowing appropriate DMs. (Eg the Electronics skill, I think maybe in the revised (ie 1980 rather than 1977) version, includes suggestd DMs for INT and EDU.) In my game, I've defaulted to 8+ for non-straightforward stuff, and 10+ for hard stuff.
As far as rolls against characteristics, I'm mostly following Andy Slack's advice in White Dwarf and using 3D-2 (gives a range of 1 to 16, so even a 1 can succeed and even a 15 can fail). But I think stat checks are relevant only for fairly basic stuff - Xenobiology is going to be more like 10+, +1 if EDU 8+, +2 if EDU A+. The rulebook does encourage the referee to keep track of these rolls and DMs to gradually build up a consistent world. This is
very similar to Luke Crane's advice to Burning Wheel referees, that setting difficulties is the most direct way in which the GM establishes the world for the players.
I agree the rules don't make it clear what EDU is for; and MegaTraveller muddies the waters with a whole lot of knowledge skills. Our game follows Classic with no knowledge skills, and we're using EDU as flavoured by PC backstory - so the INT 8/EDU 13 ex-navy guy who never got a commission but is a member of the TAS spent all his salary on TAS membership so he could travel the universe looking for signs of alien life, and his EDU is a doctorate in xeno-archaeology; whereas the two ex-military guys with INT 2/EDU 10 and INT 3/EDU 9 clearly read the manuals
very closely, but there EDU isn't going to help them much when xeno-biology is at stake. This is, in effect, similar to a background-flavoured skill system like 13th Age, but done in an informal and consensual basis - which goes back to the importance of taking suggestions from the players. This sort of system won't work well in a competitive/hostile environment where the players see their job as outwitting/out-"rules"ing the GM - but luckily that's not something I have to worry about in my RPGing.
I think you can argue that 2e DOES point GMs in the right direction in its non-mechanical presentation. I could imagine a game that leveraged the rules framework of 2e AD&D pretty well and yet was not focused on setpiece location adventure (ala modules). So, for example you could put the PCs in a milieu like 'You are all nomads roaming the Great Sea of Grass on your trusty lizard mounts' and then allow things to sandbox into tribal conflict, invasion, civilization vs barbarians, etc. It is just not the typical formulation for a D&D game, and you'd have to be willing to accommodate maybe bending some 'rules' of D&D to make it work well. Like changing the way characters are initially equipped, maybe creating more specialized caster spell lists and priest classes, perhaps a couple of specific kits would be handy, etc.
I personally think it is harder than that.
AD&D, incuding in its 2nd Ed incarnation, just doesn't generate characters with the right sort of richness and nuance to make vanilla narrativism easy. An exception is thieves - I've had success running an all-thieves AD&D game, with the focus on petty larceny and hijinks in Critwall and then the City of Greyhawk. Maybe druids or paladins would work too, but it's too hard to get a party of them without tweaking the PC gen rules.
I also think that Oriental Adventures is an exception, because it's PCs do come with comparatively rich backstories and implied capabilitiese. And the non-weapon proficiencies can play a similar role to the one that I described for EDU above. Even here, though, I think it's harder than Traveller: the default check difficulties in OA are absurdly high, which makes it harder to use "say 'yes' and roll the dice"; and if you go with WSG/DSG/2nd ed stat-based proficiencies then there is a different problem - stats come to dominate play, and players have a strong incentive to push the proficiency system into an unnuanced resolution mechanic to end-run around harder checks that would be dictated by thief skills or whatever.
Traveller, if you extrapolate from the example checks given in the books, is just cleaner for this stuff, plus doesn't have the distraction of having to build it onto a wargaming chassis (where combat always gets better but only thieves automatically get better at their other stuff).
I haven't tried vanilla narrativist RQ - I think it would sit between Traveller and D&D, as I don't think it has quite the right skill load-out to get away from the wargaming, but the wargaming is ultra-brutal. (I've GMed a lot of vanilla narrativist Rolemaster - it has the right skill list, and its development system allows players to shape their PC skill load outs, which is a type of "flag-flying" to the GM.)
unlike D&D, Traveller is a very 'gritty' game. It absolutely supposes that the world is entirely realistic. Its combat system for example is actually QUITE realistic, given the limitations of RPGs and their gamist needs. Being shot with a pistol is damned hazardous! Maybe SLIGHTLY less likely to be instantly lethal than in real life, but not by much (IIRC a basic pistol or rifle does about 11 points of average damage, and a PC has about 20 points before instant death, there are no 'critical hits', but a good damage roll on a physically weaker PC could kill them). The point is, it is expected that locations and the elements of society and government will correspond to some imaginable and realistic (at least plausible) pattern. So there will be laws, rules, administrators, economics, and other such things. In a sense these simply ARE the 'challenge' of Traveller.
If you think about it, the typical situation that the rules generate is a motley assortment of ex-military types all huddled aboard some 200 ton Free Trader that can just about make its mortgage payments if the crew is willing to take no pay and not be choosy about what sort of cargo/passengers they haul (passengers who have a finite chance of deciding to make themselves the owners in mid-jump). Their greatest threats are law enforcement, bureaucrats, and the machinations of various nobles and megacorps with whom they might have the misfortune to cross paths. Most of this means negotiating, bribing, duping, concealing, and other such nefarious activities, interspersed with hair-raising instances of death-defying battles, ship malfunctions, and maybe some weird alien encounters or more classic location-based adventures.
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I described the 'typical party' above, but the game doesn't honestly seem to put that forward as an INTENDED setup, it is just 'what happens when you unwrap the box and start rolling on the charts'. So, in a sense it is a 'looser' game. Frankly, given its focus on a modestly gritty realism, you can quite easily invent variant milieu in Traveller, like a pre-starflight game of planetary exploration (just build TL8 ships, not ENTIRELY realistic, but if you add a few details to the ship rules you can come close enough). You could do a variant game where the PCs are part of an isolated colony with no contact to galactic civilization, perhaps even one with a 'fallen civilization' or something (though now you would have to really hack the chargen rules a bunch, non-trivial but pretty easy to envisage working with say some pre-gens).
I gues the point is, Traveller is a BIT more flexible than D&D, but perhaps more in terms of convention and some characteristics of the milieu than due to any significant rules innovation.
I agree about the default Traveller party, although once you add in Citizens of the Imperium it gets a bit more varied. For me, what is more significant compared to D&D is the implied setting and hence implied challenges. If the default challenge is orcs in a 10' room, pulp movie cultists and chess puzzles, it's hard to build serious story. How does any of that relate to character motivation?
Whereas trying to make a living, getting recruited by terrorists in the restaurant at the Travellers' Aid Soceity, dealing with officials who have actual worlds to govern: that's more promising raw material for buidling something out of, I think.
You can try and add it into D&D, of course, but then you get the problem that PCs have no connection to it by default (due to lack of background/lifepath for most PCs - again, thieves, paladins, druids and monks excepted to various degrees), and they also don't have the mechanical capacity to engage with it via "say 'yes' or roll the dice".
I'd note that even BRP and Traveller have a few 'extra options' that apply in combat that aren't normally present with non-combat, like dodge/parry checks and such. These still follow the normal check rules though, and I'm sure you could say that they could be extrapolated to other analogous situations in either game (IE some sort of opposed actions).
I'm using opposed checks in Traveller. The odds of one 2d6 roll beating another is very slightly better than the odds of rolling 8+, so it seems to work OKI.