Depending on how you define "choose your class", Golden Sun: Dark Dawn qualifies. Your characters' classes (and thus, their stats and Psyenergy/spells) are dependent upon how many of each of the elemental Djinn the character has equipped.
Disgaea doesn't let you choose a class for the main characters, but you aren't ever forced to use them, and for any of the generic units you create, you get to choose a class, which you can also change later (although if you do, you start at level 1 - albeit with boosted stats). As for your second requirement, there is at least as much post-game stuff to do as there is main plot, several of which will get you special endings, and the game has a New Game + feature.
Soma Bringer allows you to choose a class at the beginning of the game, which determines what weapons you can equip (and thus what skills/spells you can get) and your character's stat growths. I'm not sure if you get to change later, though, or how much post-game content there is.
Phantasy Star Zero also allows you to choose from one of three races (Human; Newman, an elf-like genetically enhanced clone race; or CAST, an android) and three classes (Hunter = melee, Ranger = guns, & Force = mage) at the start of the game; however, once you pick your race & class, it's set in stone. There is plenty of post-game content, however, including the ability to re-play story missions at a higher difficulty, and you can transfer items to a new character if you decide you don't like the one you're playing.