I think my overall biggest beef with Chrono Trigger is that sometimes you're left with absolutely no clue where to go whatsoever, and no way to get a clear clue either. There are a couple of puzzles that come down to sheer trial and error. I think other RPGs of the period do this better, and certainly RPG design has improved a bit in that department as well (see DQ9).
Aside from that, once you get to time travel Chrono Trigger is pretty fantastic. I wouldn't call it the Best Game Ever (and I don't think that I would have called it that at the time either; it'd have to take a back seat behind Super Metroid and FF VI, and probably Super Mario RPG as well), but I'd attribute that more to my leanings towards the darker art style/feel of Final Fantasy than the lighter art style/feel of Chrono Trigger.