Back in the 3.0/3.5 days I wrote an essay listing the things I loved, things I hated, and things I had mixed feelings about. Posted here:
D&D 3E/3.5 - Retro-cloning D&D 3.0
And here are some additional issues I have, despite 3.5e still being my preferred D&D version
Issue: The exacerbation of the Linear Fighters; Quadratic Wizards" problem, due to "double power ever two levels" power scale. 3.5 purports to handle this issue by handing out loads of magic items, but I find this unsatisfactory.
Issue: You are always someone's mook. My view is that PCs beyond 4th or 5th level and the equivalent non-mook NPCs and monsters should be basically immune to one shot kills from anything short of a literally Epic opponent. But the "double power every two levels" power scale means that a 11th level party is just as screwed by a CR 18 encounter as a 1st level party is by a CR 8 encounter - mostly because of the total power of MORE MAGIC.
Issue: The expectation of generous increases in ability scores while leveling up, along with an expectation of low-level PCs having relatively low ability scores.
Issue: High Level Numbers Divergence. I don't mind high level characters having big numbers; I blow raspberries in the general direction of "bounded accuracy." I do mind when high level characters have big differences in their big numbers, especially when those big differences cut in the wrong direction. E.g. when the differences between the big saving-throw numbers and the big spell DCs diverge in the wrong direction.
Issue: Armor Class starvation. This is special case of the High Level Numbers Divergence issue, made worse by being a deliberate design decision. I see monsters being handed Natural Armor with a free hand, especially at higher hit dice, I see three or four of the "Big Six" must-have magic items being AC boosters, and I conclude that PCs don't get enough AC for player fun.
Issue: Incentives to "Christmas Tree." The cost structure of magic items is one driver of the PCs going Christmas Tree with their items, with good magic items (+2 or +3 weapons/armor, or wondrous equivalents) costing MUCH more than lesser, +1 equivalent items. Another driver is the need for certain items as character survival and player fun imperatives.
Issue: Save or suck looms larger at higher levels. This is a subset of the "you are always someone's mook" issue, made even worse by the divergence of save bonuses vs save DCs against higher level effects.
Issue: Disagreements over the place of skills in the game. Me, I
love skills, and was really happy when 3.x showed up with a skill system that was actually halfway decent. I just wanted to streamline it a bit and fix a few issues. But one trouble is that the designers seemed to have mixed ideas about what skills were for and how they ought to work. Another trouble is that many GMs and players want to "fix" the skill system by nerfing it.