RageBurner
The Struggler
Fire Emblem - I'm not sure if this would be considered a feature or not, but the way stats level up in the whole series. It's a bit less obnoxious in the newer games, as you practically trip over stat raising items, but it's a problem in the older games. Yeah, you could get lucky and roll a monster, or a good character could turn out worthless, even the main character! You get a steady supply of new characters to mitigate this a little bit, but you can't grind in the earlier games, so you have a very finite supply of EXP that could get wasted on characters that just got unlucky. That's happened to me more than a couple times.
I don't have anything against random stats, Suikoden, Final Fantasy Tactics and Chrono Cross are the three examples I can think of off the top of my head. But in those cases, characters will still end up roughly the same. I've heard some people say it makes every playthrough different and I guess? But when you play on harder difficulties where one stat point is enough to make a character double and be a good character or be basically useless. It has never stopped me from playing, but I hate it. x)
Bloodborne - I've brought this up elsewhere, but the Blood Gems can fuck right off. The idea is great, but the execution is not. You can usually get enough decent gems to make one or two weapons okay by playing through the game normally and with the DLC, but you might not even get that lucky. Sure you can switch gems around for different weapons and stuff, but I like having a selection of weapons on me that I can switch to on the fly. And the difference between a decently gemmed weapon and one without is significant. So you have to grind in the Chalice Dungeons to get a chance to get a good gem. I've done the grind on my main character, but it wasn't worth it. x) Dark Souls 3 did weapon customization the best.
Pokemon - EVs, Natures, IVs and Personality can all go to hell. Some Pokemon can be hard enough to catch as is, let alone catching one that happens to have the right combinations of stuff. That or you can breed for the same thing. I guess it's a big thing for PvP players or people who just like numbers going up. Thankfully (?) the games are easy enough nowadays that you can beat them without ever worrying about it.
Final Fantasy Tactics Advance + A2 - No it's not the Law system, I could take it or leave it. It's how you learn abilities. The concept is just fine, it never bothered me in FFIX, though it's not my favorite way to learn abilities. It's just balls in the Advance games. Boy it's great when I unlock a class and don't have any way to give them abilities! Or you're just stuck with one or two abilities for who knows how long. You still need AP to learn the abilites too! Marked One, what the hell?! I beat the original FFTA way back when, but FFTA2 always ends up boring and annoying me because of this and thus I've never finished it. Anyway, it's a shame because both Advance games are quality stuff, even though they can't touch the original FFT. >.>
Resident Evil: 0 - Not much to say on this one. Item dropping just super duper sucks compared to item boxes. It gets to be an absolute nightmare if you want to collect your items in one area, or annoying as fuck if you leave them and backtrack to get them when needed. The game has other flaws, but this is the big killer for me. It's the only mainline RE I've not beaten, so I'll suffer through it eventually.
Front Mission Series - Ah FM, my beloved. It's not a perfect series, but it's super damned good. One thing has always gotten on my nerves, however. The way to gain money outside of the story missions. It comes in two flavors, the battle simulators and the arena. The battle simulators give you barely anything and you have to manually play a whole battle. Hopefully you didn't need too much for that new wanzer part or upgrade!
But the real problem is the arena. It's like playing a shitty version of Salty Bet except you're betting money that you actually need for shit in the game. If you fight weaker opponents, you'll get peanuts. If you fight stronger opponents, you might get lucky but chances are you'll be stomped. The worst part of all is the AI in 5. It's rare that I get super mad at games, but the arena in 5 has done it on more than one occasion. Your AI pilot just makes such stupid and baffling decisions. I've lost so many battles because they decide to spend each turn running from the super damaged enemy, which causes them to get blasted every turn. I don't usually use save states, but it's practically required before every arena battle.
Another feature I hate is the Survival Sim in 5. I started writing out what it was in detail but I'd be going on for another paragraph or two. In short, it's the only way to gain lots of unique parts for your wanzers as well as the only way to grind RP (RP also sucks because you get so little of it normally that you might as well not bother unless you grind for it). It's a neat idea, but all the fun is sucked out of it. Ick.
Finally, I agree with the above points of the demon negotiation in SMT and forced party members in Suikoden blowing chunks. Why do I let myself ramble this much? Jesus Christ. x)
Yeah, FE stat growths are somewhat assinine in the design, but like you said it used to be much worse in the past.
I dislike EVs/IVs and all that jazz too. I always thought how funny the dissonance was between the anime and the game, how one completely invalidates the message of the other. The anime tells you Pokémon are wonderful friends that will share a lifetime with you, the games posit that Pokémon are fighting machines that need to be selected, bred and trained for perfection.
I do take issue with the law system in FFTA even though it is integral to the design. A2 fixes it, but then adds the stupid bazaar system of unlocks, so it's a zero sum, as far as I'm concerned.
I recently saw a friend play through RE0 and honestly everything about it feels like a bit of a mess, almost like a fanfic that Capcom decided to sell.
I love FM too but you're right, there's absolutely no good way to grind. I kind of wish you had something like Shining Force's Egress.