Going to get Crono is the first thing I do before any of the sidequests. Luminaire rulz.
As for a main character dying or sustaining some horrible injury, it's been done so much it really isn't all that surprising anymore. They did it in FFIV, which no one paid attention to. FFVII was really the last time a main character death or other outrageous event surprised anybody; they'd already done it in Chrono Trigger the year before. I know a considerable number of people who foresaw Knights of the Old Republic's revelation that the player character is in fact Darth Revan (it's well known enough that no spoiler warnings should be required) by the time they got to the second planet. In FFVIII when Edea stabbed Squall with the big old hunk of dry ice that some stoned raver DJ must've left lying around, I was like "meh, he's fine" and ordered out for pizza. Eternal Darkness is the only game that's managed to surprise me in the brutality of the villains; they kill player characters left and right in that game. In fact, only three or four of them (there's about a dozen) actually live to tell the tale. This is partially why, from a storyline standpoint, I've adopted the "brutally assault a character's sanity and emotional stability with more bloody violence and offensive epistemology than you can shake a stick at" approach.
Earlier, Zeality and I discussed fusion with the Entity as a possibility for Gaspar. It's something you see people try to do in a bunch of different RPGs; in FFVI, Kefka swipes the Statues and yoinks their power, in FFVII Sephiroth schemes to become a god, or at least some kind of higher being, by fusing with massive amounts of Lifestream. Even FATE hoped to evolve into a new species by fusing with others. But how often do you see good guys trying to obtain godlike powers? How often does a person try to become a god so they can give us all a tax break, build new libraries, devise a perfect educational program for the entire world, or even just sit back and do nothing? To my knowledge, it hasn't been done. If this is what happened to Gaspar, but he hasn't destroyed everything already just for the hell of it, what does that say about power and who people are?
DDK and I were discussing the actual ramifications of an End of Time the other day. Lucca effectively says that singularities are used to engineer Gates. Well, if everything collapses back into a singularity at the end of the universe, what would happen then? Does the End of Time exist as a place of mere thought, or does the universe loop on itself not just spatially but with regards to time as well? If all matter in the universe is present in the singularity at the End of Time, theoretically all possible spacetime continua should be drawn in. Furthermore, it's never really explained why Lavos is having such a powerful effect on the fabric of time, or if the answer even if Lavos, though from what we've seen of his thirst for power it's a safe bet he's the perp.