One of the big complaints about 3.x was how unbalanced the game could become given the ability and propensity of some players to create mechanically optimized builds. It is pretty clear that this was a major consideration in the creation of 4e.
What, though, if you want to play a 3.x game and are still concerned about this? One solution might be to place caps on things. Off the top of my head:
Maximum bonus to any d20 roll = (2 x ECL) +5
This would apply to skill rolls, attack rolls, caster level checks, saving throws, etc. If your bonus would normally exceed this, just use the maximum. This would require some tweaking of magical effects that provide massive skill bonuses (like Jump or Glibness) so that they would function differently.
Maximum damage to a single enemy in a single attack = (5 x ECL) +15
Attacks that were optimized to do damage beyond this level would still have value insofar as they’d be maxing out on damage more often than other attacks, but it would cut down on the massive imbalance that is currently possible.