Or maybe - just maybe - I actually play the games, and can comment them as a result?
TBH my biggest beef with 3.5 is the bindings. The fact that my shitty Arduin book is holding up better than it is a joke. I don't take any of the old D&D books except 1E out of storage and just use PDFs for them, since they're pretty much ruined.
Campaign setting splat-books. Dragonlance, Forgotten Realms, Planescape, Spelljammer, Dark Sun, etc.
Things like hit dice, damage, and a lot of other stuff are still based on other dice. The d20 is the basis for attacks, skill checks, and a lot of other things though.
Mechanically, the main "flaw" in a d20 system is that it's always linear - though seeing as this is the case for most things in every edition, that's not necessarily a flaw of its use in D&D, but more a flaw in other games trying to use it just because D&D does. The 3d6 system, for instance, would have a curve - you're significantly more likely to roll 9-12 than 16-17 or 18. This allows you to set challenges in much more interesting ways, and tends to give a lot more flexibility. A good system cuts down on the math done in play by doing it all outside of the game.
Now that's all in abstraction. What about D&D? In that case, the d20 system takes its flaw from the scaling upwards of numbers, something which began in 2E (albeit at a much lesser degree) when the matrix system was deviated from. The Immortal's Handbook is essentially the problems of this system taken to their absolute illogical extreme, to the point of being completely unplayable. In-game, are just a little fucked by it.
Essentially, in earlier editions, monsters generally keep within that range of 0 to 10 for AC, and powerful ones have negative ACs. While monsters at higher levels will have more HD, it's only the "big bosses" that are continually harder to hit past a certain point, and even that is eventually surpassed at ultra-high levels. d20 keeps things scaled, in order to match player growth. A Fighter at 20th Level is about as likely to hit as at 1st Level (4E does this as well, but it's a little fucked).
House-rules can fix it, but even then, the comparatively poor scaling of damage vs hit points caused by the system for everyone that isn't a spell-caster just fucks things over.
4E is pretty much the only system that needs a board. Combat is a lot more tactical in terms of movement, and the game is "balanced" such that classes are generally on par with each other. The large amount of content in Dragon magazine and splatbooks (though not 2/3.5-tier) means that some options are definitely better than others, and "tiers" exist to some degree, but it's not too noticeable in practice.
If you have a group that's willing to learn all of the rules, the space to set it up, and the willingness for very slow play (or very fast players), it can be a fun fantasy battle simulator. If any system was to be adapted to a video game, it should be 4E. But if I'm going for an actual RPG, I would rather the OSR style every time, and the mechanics of 4E simply do not lend to that without very heavy adjustments.