So, FFVIII wasn't really my cup of tea, although I had some fun playing it.
PE2 is quite different from the original, which I personally found to be a little offputting, but the more RE-style gameplay may be a positive thing for you. I've been meaning to go back and give this game another chance, especially since I absolutely LOVE the first game.
Chrono Cross gets my vote completely. Despite the confusion, it IS a sequel to Chrono Trigger, although the connection is pretty vague. The connection between the two was made more clear if you've beaten the DS version of the game with the new final dungeon. Either way, this game easily stands up as the one to play of the three listed for a large number of reasons.
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