Okay, I just finished losing to the final boss with the Lucca/Robo combination for the second time. After it cast meteor on me twice in a row I gave up on winning that ending because that fight is unreasonably hard. Yes, I know there's a bug and Ayla should be there but I've given up on that thing. I beat the other endings and found only Crono's ultimate weapon, but I played a good chunk of the game.
My thoughts on the game is that it's okay, but riddled with flaws. The story is okay, but it's lowered a lot by poor pacing and characterization. The whole "OMG LAVOS" at the beginning is an example of things happening on too grand a scale waaaaay too fast. There are certain plot moments in games that made me step back and go, "You know, this is pretty ridiculous." That moment was on the same level as the whole "I have an evil twin brother" thing in Final Fantasy XII and the whole "We're all from the same orphanage and the sorcress was our babysitter but we got amnesia from our summons" from Final Fantasy VIII. And yeah, Haste never working was annoying.
That said, I think there were some very cool parts of the game. I totally dug the first forest map and the 2300 AD map. The background music was pretty kickass throughout, and I did think the King Zeal boss fight was a pretty inspired move, and pretty awesome. Actually, all of the boss battles in the final dungeon were pretty awesome. The Magus fight was pretty cool too, but the whole "controlled by a magic spell" thing was on the same level of the other plot devices mentioned above.
The nice thing about Chrono Trigger/Cross is that with the whole "parallel dimension" thing, you can basically consider any fan work a form of canon in just another random parallel dimension. I think this is a nice contribution, but I'd reconmend making an updated version and fixing a few flaws. Also a cool idea would be an optional boss battle with Goku (unless there is one and I just didn't find it). At first the Goku's grave thing fell into "evil twin brother" category, but I thought to myself, "You know, that'd be an awesome boos battle.