I am pretty harsh on most of the things described, much moreso than DJ or Dhyer anyway.
1. Above endgame levels: almost always not. Who cares if Guv gets more damage at Level 64 or whatever, you're nowhere close to that. Terra learning Ultima at Level 99 is an obscure point of trivia. etc.
Fei's Yamikei is much worse than people normally give it credit for, you have to power-grind deathblows in addition to grinding levels. Kokei is also terrible. Both skills give Fei an advantage he never enjoys in-game, they can screw off. It doesn't help that Fei is actively awful at learning DBs in-game.
VP2 Lezard gets Heal, WTF? His level is fixed! I mean, if you want to allow it because you allow aftergame stuff, okay, but you'd better allow those! He never has Heal outside the aftergame.
No Time Gate/etc. either. More stuff which is "unique" because some FAQ said so, I certainly never got it and nor did anyone else playing the game in a remotely efficient way.
As far as I'm concerned, the only reason to be lenient on this front is if a character is close to getting the skill at endgame level. I allow Terra and Celes their L3 spells because they're close, and would do the same for Kokei if level were the only block for getting it. It helps that in Terra/Celes' case, it represents an advantage they hold in-game, their high magic stats. (Too bad about Relm...)
2. Rare drops: It depends on "A lot of grinding" I guess. I'm pretty okay with Katt's MeowST because it doesn't seem that unreasonable to me, it's roughly 1/32 per 2-Carm formation and those are extremely common. But 1/128, or a rare/hard-to-kill enemy, would push this to "no" to me, like the BoF3 Goo King Sword.
3. Class-unique stuff: You know what doesn't define a class? Colour-corresponding elements in CC, which PCs of one colour don't use better than those of any other! (Except the ones which are actually locked to PCs of that colour.)
S3: Anything which rewards A+ had better reward A as well, or neither, since I'd rather have the latter in-game. A+'s are dumb with their ludicrous CP requirements, I'm honestly inclined to cap them below A+ except that Thomas doesn't really need to suffer more. I'm a bit leery at handing out more magic runes in most of these games though because the "1-2 shots of L4 damage" gets really overrated in the DL compared to in-game with the total lack of MP healing, and I'd rather not have duellers like Mel exacerbating this. (We already have to live in a bizarre alternate universe where Piccolo is a better offensive PC than Borus, that's bad enough.)
As you can tell I'm not a fan of most of this category. It often relies on wishy-washy arguments which aren't applied consistently, they are more arbitrary and less intuitive and don't honestly change duelling casts in a way I'm a fan of anyway.
4. I generally assume knowledgeable players (fewer debate that way), so this one isn't much of an issue for me. If something is already borderline, though, this could be part of an argument for disallowing it.
5. Uh. Um. Maybe? It'd have to be something I'd be willing to buy an average player to do, though. Like... I'm okay with holding shamans against the final BoF2 bosses because wanting to fight the endgame in your super-badass forms seems like something a number of players would want to do. If, however, it was a matter of redoing the final dungeon in order to get one character 5 more attack, or something, I'd probably not consider it. I dunno, this is probably case-by-case for me, but I can't think of too many instances where it comes up. I guess one example would be that I wouldn't allow Mog/Edgar both the Aura Lance (you can get a second by leaving and betting a Sky Render), though that has the extra problem of Cyan kinda wanting the Sky Render anyway (in case he's berserked or against low def).