Li Shenron
Legend
I think the reason that penalties don't exist is that penalties aren't needed.
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Not only is this more streamlined and easier to assess than a list of plusses and minuses, but I feel there is a psychological aspect as well. Penalties aren't as fun as bonuses. It doesn't really matter, I know, whether you give someone a -1 or not give them a +1, but the perception of a penalty is that it is a negative thing to be avoided. So it does matter to some.
The question in my mind isn't really why didn't they add penalties, but why should they? The only reason I can think of is nostalgia, and that's not a good reason IMO. If your reasoning is that they should do so because their targets are wrong, then that's really a different debate...given the goals they had, I think using only bonuses is pretty elegant, at least with the races we've seen so far, and with the assumption that their goals are what I believe they are.
Well apparently they were needed a long time ago, to differentiate the races for narrative or strategic reasons, while maintaining a basis of 0 for the humans. Thus not NEEDED in the strict sense, as pretty much nothing is strictly needed in every single RPG ruleset.
Indeed the psychological effect is there, and perhaps it is even the most important one, since increasing everyone by +1 can be effectively nullified by increasing the opponents (NPC and monsters) as well, but the feeling delivered can vary.
Ultimately, ability score penalties are unneeded just in the same way that ability score bonuses are unneeded. People want them for the feeling, and that explains the general trend slowly upwards across editions, every "new" product trying to deliver the subtle feeling that "your character will be better than before".
Narratively, there has always been the idea that races are different, so maybe elves are more agile but less robust than humans, or dwarves are more robust and less agile (or whatever, depending on the concept which might even change between editions). Core playable races are wanted to be on par, so it was easy to design them so that average human characters set the zero level, and other core races have a bonus here and a penalty there for a net zero average again. Feeling notwithstanding, that is IMHO the truly most elegant design, but eventually WotC designers value the sugar feeling more in this case. From a mechanical point of view, one way or the other doesn't matter much.