I GM more than I play, so I have the GM power to rule-zero out the parts I don't like.
Right now I'm running a "Brotherhood of Rangers" campaign where the PCs are all gestalt-rangers (fighter-ranger gestalt, wizard-ranger gestalt, cleric-ranger gestalt, etc.) I'm trying to keep the house rules in this one down to a minimum, with the biggest change being to disallow a list of teleport/travel spells that would ruin the "ranger" feel (IMHO). The second biggest would be allowing feats instead of favored enemies - none of my players wanted favored enemies if they could have feats instead.
For a more general D&D game, I'd have more house rules - but still many fewer than in earlier editions. And I'm meh-to-yuck on Pathfinder, 4e, and 5e, so when I run D&D, it's going go be 3.5.
I have an old (c. 2006) rant about 3.x that I might as well unload here:
The Things I Love and Hate about Third Edition D&D
(AKA the Good, the Bad and the Ugly)
This rant has been building pressure in my head for some time, but only now has it burst out in actual written words. It's divided into three sections, the "Things I Love" about 3.0/3.5, the "Things I hate" and the stuff I have mixed feelings about.
Things I Love
1. Skills: At last D&D has a decent skill system. I have quibbles about it (e.g. the cross-class penalty being too big), but my quibbles are just quibbles.
2. Feats: I first went "huh?" when I first encountered them, but they've grown on me since as being a really good idea.
3. A set of battle-mat combat rules actually usable by Mere Mortals, as opposed to the 1e rules that were only usable by Total Wargaming Geeks, and that most players (including myself) therefore ignored.
4. The d20 mechanic itself: A nice job
5. The general rationalization and simplification of saving throws, xp needed per level, ability score bonuses, etc.
6. The rules for creating magic items, and the wealth guidelines in general. It is a good thing that the rules no longer try to stupidly pretend that a +1 sword is a [reverberation]BENISON BEYOND PRICE[/reverb] And I have no sympathy for the DMs who whine that they can no longer act like Gawds; that they no longer have the unquestionable authority to insist that their players smile and say "thank you sir" if they choose to inflict such poverty and suffering on the PCs as would make a sane person envy Job.
Things I Hate
1. The double-power-every-two-levels power curve: Works OK up to about 8th level, starts to break down at levels 9-12, completely wonky at levels 13+
2. Magic as a Trump Card: The general philosophy that has magic trumping non-magical abilities, and that only more-powerful magic can counter less-powerful magic. There are exceptions, yes, but they strike me as being rare and grudging.
3. Disposable/expendable magic items: Some items do have to be consumable, like potions or scrolls. But I find it annoying that so many other items are consumables as well. Wands. Staffs. A lot of the miscellaneous magic. And it really bugs me that it costs xp to create those consumable magic items.
4. Spellcasters as the ultimate source of all good things. This is related to (2) above, but the issue would be less annoying if non-spellcasters had a greater ability to create magical or otherwise special items. For example, if crafting magic arms and armor were something fighters could do. Or possibly even something they could do better than wizards.
5. Prestige Classes. Bah! I say, and Bah! again. They're munchkin-bait; things that actively encourage the unspeakable practice of trying to produce the uber-build. ("Rogue 1/druid 1/milkmaid 2/divine rennet 1/munchkin cheese 15 - ha! Let's see you beat that build")
Mixed Feelings
1. The great number of magic items that characters have. Yes, magic items are a necessity given how D&D is set up to be a high-magic game. I'd prefer, though, that characters have a smaller number of really cool & powerful items, rather than the larger number of weaker ones that the game gives by default.
2. Multiclassing. In some ways 3e fixed multiclassing, and made it sane and rational. In other ways, it created new problems (with those unspeakable "prestige classes" then being offered as the kludge to "fix" those problems).
3. The rigidity of the wealth guidelines. It would be nice to have an analysis of just how much extra wealth boosts a character's power, and just how much relatively poverty diminishes it.
4. Rangers. I imprinted on the 1e ranger as "the" ranger, and I though the 3.0 ranger was almost perfect - it just needed to be a little less front-loaded, and to have more combat flexibility than that hard-coded TWF ability, and it would be good to go. The 3.5 ranger felt like a step backward to me; a change to "wilderness ninja" from "Paladin of the Forest" (Which is what a ranger should be, in my completely arrogant opinion). And that TWF or Archery choice, while an improvement, still felt like a horrible kludge.
5. Healing. Healing via divine magic is such a deeply rooted D&Dism that any change will have huge, far-reaching effects. On one hand, I'd like to see less dependence on the party medic, er, cleric. But on the other hand, it just wouldn't be D&D without this element.