w/r/t Point 1. I won't dispute that you can use D&D to play a ghost, vampire, Kaiju, or disembodied intelligence. I don't think the game handles these options very well, because (a) there isn't a lot in the way of rules for doing so, and (b) non-human characters tend to upset/conflict with other assumptions in the rules about how the game is to be played.
I disagree with (a) because there are alot of rules for handling ghosts, vampires, kaiju's and disembodied intelligences as NPC's, and in 3e at least, the rules that NPC's are under are virtually identical to those of PC's. I'll come back to 'b'.
Consider the vampire -- an iconic monster that people like to play. But the D&D vampire makes a really weird PC because of its mix of powerful abilities and crippling weaknesses. On the one hand, at-will level draining gives the vampire a huge offensive advantage. Damage reduction gives it a significant defensive advantage. At-will gaseous form gives it a powerful tool for avoiding traps, sneaking past enemies, and general exploration. Put this vampire in a typical dungeon crawl, and it is nigh unstoppable...At the same time, the vamp has critical weaknesses. Sunlight and running water destroy it. It cannot enter private buildings. It's tied to a coffin full of dirt. These weaknesses, deform the game experience. The vamp can't meet NPC's in the broad light of day. When it travels, it has to keep up with its coffin. When it dies, it can't be raised.
But this isn't a problem with the rules. You've just outlined in detail the exact contridiction to what you've asserted. You just asserted that there aren't alot of rules for handling vampires, and gone on to list how the rules handle them in detail in a wide variaty of situations. You are disproving your own point.
What you have actually demonstrated is point 'b'. If the party is playing vampires, then chances are you will have to tell different stories and provide different challenges than if the party wasn't playing undead, blood-sucking monsters with vast supernatural power. Isn't that however a good thing? I would assert that the rules obviously didn't handle vampires well if a character played a vampire and it made no effectual difference in the stories that the game supported. The fact that the stories have to change in responce indicate that the rules at least handle the vampires fine, and its really then a matter of whether the game master handles the stories well. Whether a game master can handle stories with vampires, godzilla and disembodied intelligences well is a different question than whether the rules can handle it. Whether vampires actually provide a good medium for stories and whether the game master can imagine and run those stories is independent of the rules involved.
In my opinion VtM tended to fail precisely because almost no one really wanted to be involved in a vampire story, so they ended up playing sessions of D&D were people happened to be Vampires in name but were simply black wearing superhero adventurers in fact. The rules in my opinion actually couldn't handle the central story that they ostencibly provided for - namely the exploration of what it meant to be a monster and the eventual denounement of the monster whether by redemption or death or both.
What does a disembodied, super-intelligent alien intelligence even do (other than torment Captain Kirk)?
But this is a story problem with playing disembodied super-intelligent aliens regardless of what game system we play. The problem with playing radically non-human entities is always our ability to relate to, understand, and care about what ever it is that these entities care about (if indeed they could be said to have emotions like 'caring' at all).
But I'd point out that there aren't a lot of rules support for, call it non-adventuring play. And what rules are out there are often fairly thin and poorly developed. Or long out of print. The focus of the rules is on adventuring. A group that isn't adventuring is ignoring big chunks of the rules (character classes built for adventuring, combat and adventuring equipment in the PHB, the combat rules, combat-oriented magic, etc. etc.) They may find themselves having to create significant houserules to do what they want (frex, creating an economic system that makes sense).
You point about the economic system is well made, because its one of the things that I think the rules really don't handle well and has been an objection of mine to D&D for nearly two decades now. However, many people - including myself - would argue that good support for RP centric play is precisely a very rules light approach. IMO, you don't want alot of dice rolling cluttering up a role-playing scene. At most, you want a conflict resolution roll occuring at the scenes climax or end. IMO, D&D's light social rules and flexibiilty over whether you use fortune at the beginning or fortune at the end (or both) to influence the situation mechanically are ideal in any RP heavy game. Systems that are rules heavy about non-combat situations tend to cause RP scenes to play out very much like combat scenes, with alot of dice rolling, meta-tactics, and meta-language communication and this just gets in the way of what you are trying to achieve. Ironicly, this means D&D may handle RP centric stories better than systems created to be RP centered, because often the designer thinks to support RP centered play you need the same sort of rules heavy crunch for role playing that you see in D&D for combat.
If I had to make an objection to D&D as a RP centered game it is that the combat system (because its both abstract and simulationist) gets in the way of RP centered combat. But if the story isn't combat heavy, it's relatively ok that it doesn't handle combat 'well' because that's not what the story is about.
D&D is built for melee combat. Many monsters lack ranged attacks, which makes them particularly vulnerable to ranged weapons. Combat in a dungeon environment takes place at extremely short range, making it hard to get off more than a shot or so before melee begins.
These objections aren't specific to guns, and seem to me to ignore how D&D is actually played. Quite early on, using the default rules, PC parties will find themselves highly advantaged at range vs. most monsters and in particular at very long ranges. In many games, combat in a dungeon environment is the exception and not the norm. So very many games I've played involve the PC's acting very much like teams of elite snipers and trying to initiate combat at very long range. Any DM with much experience at all knows that he can't use non-flying brutes without ranged attacks in the open versus a mid to high level party, because they'll simply outrange it or take to the air and pelt it to death. The presence or absence of guns don't change this at all.
For genre reasons, which are largely illogical, folks tend to overestimate the lethality of firearms while underestimating the lethality of, say, an axe to the face. In other words, folks I know do care that an enemy can survive 15 shots from a handgun even though they don't care that the same enemy can survive 15 blows from a longsword.
This was exactly my point about firearms.
D&D generally assumes that combatants will protect themselves with heavy armor. This causes a problem with modern settings where heavy armor doesn't really exist.
This is a problem D&D rules have that has nothing to do with firearms. D&D requires patching to a greater or lesser extent if you change the default genera even as much as moving the setting to an African or Central American pastiche. This has nothing to do really with firearms, which are easily patched relative to heavy armor IMO without changing any rules unrelated to firearms, and more to do with D&D having little or no active defences and relatively poor rules governing shields.