Heck, in the case of psionics the various psion disciplines were all keyed off different abilities, including strength, dexterity, and constitution. From all I've read about it, it was actually fairly balanced that way.
3.0 specialist disciplines were pretty balanced. Unfortunately, they were the ONLY part of 3.0 psionics that were. Wow, that system was messed up...especially in the case of a psionic character vs a non-psionic character...psionic combat was brutal on your PP total.
For the record, I have 2 groups that I play in. One, I'm a PC, and if you roll a 1 (only on attack rolls), you have to roll a DC10 dex check or drop your weapon. Minor. Doesn't make a HUGE difference in the game, especially since my PC can make that on a roll of 4+ for a total of a 3/4% chance per swing (thats .0075 or 1 in 133 chance) and he seldom attacks with his sling anyway. The other, I'm the DM, and we don't use any crit fumble rules. Roll a 1, auto-miss, that is all. And we don't miss it.
If a (variant) rule makes very little impact on your game, why even have it? If you like it, fine. If you've always just played that way, try a session without it and see if it makes the game any less suspenseful or exciting or fun. I bet most people wouldn't even miss it.
Its the same thing with Death by Massive Damage rules. Especially at higher levels, nearly every hit is 50+ damage, and even if you have a +14 Fort save, you still have a 5% chance to auto-die on nearly every hit. So what if a bad guy fails his every once in a while...he'd probably die anyway a 1/2 a round later. Its different from a death spell, since it could happen EVERY round, sometimes multiple times in a round. It just doesn't add that much more excitement to the game, and dying to a botched massive damage save is so anti-climactic. Another variant rule that I personally feel doesn't make the game any more fun, and in fact, often makes it less fun, and no one misses when you stop playing with it.