The brittle magic system, with fixed lists of approved spells, often incredibly specific in effect and therefore hard to customize to a non-trope character concept. For one incredibly basic example: Why is there no generic ranged-damage cantrip that lets you pick the damage type (acid, force, fire, etc.) when you select it? Or, if amounts need to depend on damage type for some reason, why is there no full set of ranged-damage cantrips for each damage type? The argument applies all the way up to 9th level.
By contrast, the incredibly broad set of skills, albeit each tied hard to a particular ability. Wizards may go on about three pillars, but you can see the relative sizes of them from the page counts of combat & (mostly-combat) spells rules vs. skills rules.
Races with their fixed ability bonuses. RPGs are supposedly about playing exceptional characters, but if you wanna be a great dwarf wizard, you are handicapped and can't be that exceptional dwarf without cheesing the character generation.
The need to shoehorn any character concept into one of the established ABC menu system of character classes, instead of being able to choose a set of features to fit the concept.
Combat is boring. Too many instances of "nothing happens" on a failed die roll.
Absolutely no scaling of concentration by character level. Even being able to concentrate on 2 spells by some mid-high level would make a huge difference in fun.
I'll just stop there!