I can deal with random encounters as long as the developers have put effort into other aspects of the gameplay. It's really not that big a deal, especially when the other most common encounter system in JRPGs isn't significantly better.

I wish developers wouldn't make JRPGs so linear. JRPGs have always been fairly linear from a story progression point of view but at least they would give you a airship or something at some point and let you explore the world. Then FFX reared its ugly head and most JRPGs since seem to want to put you on one path with a few sidequests off to the side at the end. I'm not saying we should bring back world maps since that would be anti-progressive but we need to see more games that are designed like FFXII and DQVIII.

I want challenge. I am sick and tired of RPGs making boss fights the only real challenge in a game (and even that is stretching it cause even most boss fights are jokes nowadays) I know people play these games mainly for the story but its still a smurfing game people!!! I feel much more satisfied when I get to that next cutscene after a grueling challenge; than when I fought some worthless joke of a boss that was literally 5 rounds of me hitting Fight to win. I also don't believe in challenges being Extras. I don't want to fight the uber powerful, "I'm a smurfing god and now you DIE!" optional boss. I want the final boss to be like that boss. I don't want to have to wait until the end of the game to unlock the challenge. I want the whole package to be challenging and fun.
Find a copy of SMT Nocturne. If you go out of your way to complete the sidequests and fight all the optional bosses, you'll not only get a better ending but a new uber final boss to fight at the end. Also, unlike most other JRPGs, the game itself is genuinely difficult the whole way through.