3.0 had some oddities that I thought were better handled in 3.5.
For example, the Improved Critical feat used to stack with the Keen Edge spell and/or the Keen weapon property. The result was characters threatening a Critical on a roll of 12 or better. (Consider the Rapier, with its threat range of 18-20. Add Keen and that becomes 15-20. If you can also stack Improved Critical on that, 12-20.)
Magic ammunition used to stack with magic weapons, so an archer could effectively have a +10 weapon.
And, of course, the front-loading problem: Many classes and PRCs had their neat features come intp play at 1st level. This encouraged fruit-salad builds who took one level each in half a dozen classes for the special features, essentially giving you Captain Everything.
Polymorph Other (the predecessor of Baleful Polymorph) had no down side. Build a Wiz type with all abilities focused into the mental stats, then Polymorph Other on yourself to obtain ultimate physical stats. There was no reason for a higher level party not to go adventuring Polymorphed into Fire Giants.
Disintigrate was a Save or Die spell. Not that bad a thing, all things considered, since it both required a successful attack roll *and* allowed a Save, but I like the new version better.