1: Usage of fanart in pages, especially when there's official art. I couldn't care less that you dislike pixel art or Peppa Pig-level doodles for your "beloved" characters, that's the best representation an author has given, and to go with whatever you find online gives a big sense of unprofessionalism, arbitrary bias, headcanon (come on, fanart is very prone to change body proportions, shades and details of a character as much it isn't meant to be faithful beyond a representation) and plagiarism out of using something without authorization of the artist.
2: How currently tier 1 is all based in perspective of a "main cosmology", so even if a setting goes normal for a good while, then the plot has a twist of it seeing Y as fictional and being regarded as higher-d in relation to it, that makes the fictional thing just tier 11 instead regardless of statements or lore, especially when by that logic we'd be nerfing plenty of tier 1 series too as they have the tier 1 thing as more prominent than the 3-D one to begin with.
3: How over half of the verse-specific powers and abilities on the site are just physiology pages, I even kinda regret being the one introducing the concept.
4: How we rate any hax that can affect a tier 1 or above as smurfy and thus inherently ignores any resistance on tier 2s and below, when that's really just range IMO, as much as being able to affect the entirety of a universe with time stop isn't inherently more powerful for the purposes of comparing to a resistance than doing so in a select area, or vice-versa. Sure, the power may travel uncountable infinities and whatever, but that'd be like saying someone with infinite speed has inherently High 3-A AP.
5: As an extension of the first point, using non-canon art for a character's main page, for example, using a Super Smash Bros render for a main canon page, it implies we accept them as the same canon when that's far from the truth.
6: Also having galleries in general, especially when it's quite irrelevant stuff for our purposes like concept art or different sorts of official art (I'll totally cringe if it's fanart) that are just the exact same character appearance with no changes to begin with, for example, featuring renders for Mario with the exact same appearance but just with different poses or style out of changes in art direction at most.
7: How the Varies tier is handled, we should have a tier for characters whose power actually varies between A and B (like Ditto), not for characters that are pretty inconsistent and just have a low-end in A and an high-end in B, the fact both meanings are oddly mixed up yet we don't allow a Varies character to be in any point between A and B for a match is just terrible to say the least. Like, "X tier, possibly/likely Y tier" exists, that'd be way less misleading for inconsistent cases than to just say "Varies from A tier to B tier" in either case.
8: How NSFW verses aren't allowed. While I can understand that it's a big no no from Fandom and all, I think there's plenty of NSFW series to index with legitimate feats and all. Like we all know how Monster Girl Quest was among the strongest 2-A series on the site, and even had plans for a tier 1 upgrade at some point. Your "Oh no, they're mating on screen" is as valid as "Oh no, he got bisected in half graphically", just don't feature these images.
9: Crossovers. Even with the recent revisions I still think the site is way too strict on their usage for any purpose, sure, they may tend to basically have both series on the same level for the sake of the plot, but that's not inherently unusable as in-plot explanations can happen, let alone with inherent powers they'd carry back not having any possible contradictions
10: Seeing users do way more than some staff members, yet never are nominated to be staff themselves.