Real Texas: It took me a while to warm up to this game because of the awful combat and interface, Albion-level awful, but it was such a unique, creative and humorous game that I soon grew to love it and it became on of my favorite C.R.P.G.s.
Tales of Berseria: This is the only Tales games I have ever played, and it made a poor first impression with a dull first stage and combat with a very flat learning curve, but when I got to the meat of the game and learned to play it I realized it was a very creative, fun and detailed game with memorable characters and settings. I know it takes inspiration from Berserk, but unlike From Software's games, from what I have seen of that awful comic it only resembles it on the surface level and has much better stories and characterization.
Final Fantasy 6: My first R.P.G. was either this or The Elder Scrolls: Arena, and it took a while to get used to it. Using giant robots at the beginning was fun, but the slow framerate in the introbeing led by the nose through a repetitive series of fights, having trouble with the unfamiliar battle system and and reading the awkward dialogue at the beginning was not a good introduction to the genre. Terra was freed and the game opened up quickly however, and then the gameplay, pacing, writing and creativity improved significantly and I realized that I was dealing with something great. This would be my favorite Final Fantasy if it was half as long instead of turning into a dull open-world C.R.P.G. at the end.
Moryou Senki Madara: An obscure NES classic--I should probably put it in the obscure game thread--but it makes a poor first impression, as the combat is barely more than bump combat--I hate bump combat--the game requires a lot of grinding at the beginning and the story takes a while to develop. It eventually picks up after the first dungeon, then you need no grinding until the end, the story becomes much more interesting, the pacing picks up and everything is a lot more fun.
Disgaea: I am not really a fan of strategy games, and the weird mechanics made it difficult to adapt, but when I did I realized it was creative and fun. It helped that I began with the first game, the best of the series.