Final Fantasy XIIIs treasure hunter trophy, this one is pretty notorious among JRPG fans. It requires you to obtain all weapons/accessories in the game but the game doesn't keep track of what you have so you have to write them down as you get them and keep a list of what you need, you'll also need a guide to tell you how to get everything because some items transform into completely new items and the game doesn't tell you what they turn into, it also requires a good 40+ hours of grinding.
Niers trophy that assumes the player will log in every day for months to cultivate his flowers, players just manipulated the PS3 clock instead. Nier also has a trophy for upgrading all weapons which requires about 40 hours of grinding in a game thats 15 hours long
Destiny's Flawless Raider trophy, it requires you to complete a raid without anyone in your party dying, this became dramatically easier after the expansions came out however it still requires 5 other high level players who want to do the trophy, which ended up taking me a year or so to do because its just so hard to find people who care about trophies and have the required gear and knowledge of the raids.
Final Fantasy IX's 1000 jump rope trophy, i never got close to doing this on a CRT TV and a wireless controller, i dont want to think about how hard it would be on modern TVs and wireless controllers.
Just as a rule of thumb, missable trophies in long RPG campaigns, as if i'm going to play through a 40+ hour campaign multiple times to get a trophy. You should be able to chapter select or clean up any trophy in post game.