Sure it is. You just make it laborious enough to do that it's a waste of time.
And how, exactly, do you propose going about doing that?
Do you overwhelm the optimizer with too many options to choose from?
Well, no, because this is the sort of environment that optimization thrives in. 3.X, even if you don't take advantage of all of the non-WotC OGL content available, offers more customization options than any other edition. It's also always had a lively char-op community. The more options that are on the table, the more opportunities there are for finding and exploiting combinations the designers overlooked.
Do you take the opposite approach and keep options at a bare minimum?
Well, this certainly limits the enjoyment of optimization oriented players, but it's not by making it laborious. The fewer options on the table, the easier it is to spot which ones are best. It also means you're taking away all of that customization from everyone.
Do you bury it in complex math?
This raises the barrier a bit, making it harder to get into the optimization game. However, for many optimizers it's the sort of thing that's right up their alley. Crunching numbers to find the non-obvious advantage? Music to their ears. For those that don't have the head for the math, once the number crunchers have the system in their hands for a few minutes, someone will share the results, removing the barrier completely. There's also the fact that you likely scare away a good chunk of those who don't pay attention to optimization, as they opt for the choices that don't require a math degree. That makes the gap between the optimizers and the non-optimizers larger.
Even if you can find a barrier, something that makes the combing through options process tedious and unwieldy, as long as some degree of imbalance between choices exists, someone, somewhere, is going to put in the effort to find it. And then they'll tell other people about it, and those people get all of the benefit of knowing the best choices, without any of the tedious, unwieldy, laborious barriers.
But it is possible to have mechanics that tend to dissuade specialisaion and encourage diversification in PC build, for example - whereas, in practice, a lot of optimisation in a game like 3E or 4e is based around specialisation.
Or to have mechanics which offer few and constrained places for player choice about build. (RuneQuest and Classic Traveller are examples of this.)
I'm not advocating for those mechanics - especially not for D&D, which historically, and especially since 3E, has taken a different approach - but they do exist.
Oh, absolutely, you can discourage specialization. I think it's even a worthy goal. D&D tends to over-reward and under-punish specialization*, I think.
Next's dropping the Fort/Ref/Will saves/defences and changing them to ability saves is a decent step in that direction. Where a 4E character can have a perfectly decent Will defence while dumping their Charisma or Wisdom stat, as long as the other gets a decent score, a Next character that dumps either is leaving themselves a weak spot that can be targeted.
Admittedly, this is counteracted to an extent by making it harder to target those weaknesses than it would be in 4E, where almost any character, monster, or NPC can find a way to target any one of your defences with a damaging attack at least once in a fight.
But making specialization less optimal isn't punishing optimization. It's making diversification more optimal. The target has changed, the process hasn't.
* Of course, this doesn't apply equally to all aspects of the game, nor does it apply equally to all classes.
A 3.X fighter is rewarded for becoming hyper-specialized in their tactics, and effectively punished for trying to diversify. A 3.X wizard can quite easily get the best of both worlds, using spell selection to decide each day whether to be a generalist or a specialist (and with enough spells to choose from, a specialist in a different thing each day).
A 4E character that tries to specialize in dealing one specific type of damage (other than the heavily rewarded cold damage) will find that it is often of little benefit, and can easily become a dangerous weakness. If all you ever do is fire damage, you better have picked one of the character types that has a way of avoiding the ubiquitous fire resistance, found on more creatures than pretty much any other damage resistance. Meanwhile, unless you know you're going to be dealing with wall-to-wall trolls, you're not going to encounter all that many enemies who care about the difference between fire damage and untyped damage in a way that hurts them more than it hurts you.
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Any time that player choice exists alongside imbalance, optimization will be rewarded.
You can remove imbalance, but it takes a good deal of effort, constant supervision, will never be perfect, and lots of players seem to take issue with the idea.
You can remove player choice, but it makes the game a good deal less interesting, and it's simply impossible to remove entirely.
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