I got bored with reading the entire post (I got up to page 16 I think), so I'll post what I have to say now
However, after spending so much time reading replies I've forgotten what I had to say about the plot and stuff...
Anyway, is it possible to put all the plot into one post? I printed what was in that seperate post for plot, but that was before I realized there were various posts of plot here...
Is Glenn supposed to have new weapons besides the Masamune? Maybe instead of having him lose the Masamune to be replaced by new weapons Melchior could upgrade it somehow, maybe by infusing it with magic, or reinforcing the blade with new material or something (maybe you can obtain materials like in CC)
Also, I never really used Lucca except when you had to, so the topic of her weapons never crossed my mind. How come no one else (besides Porre at this point) in the world can wield a gun, yet they can manufacture them to sell to Lucca? I think it'd make more sense if she created her own guns, maybe with the same kind of material system...
Who is Atropos? Was he/she/it in CT and I just don't remember him/her/it?
Alright, on to what I remember of the questions I had concerning the plot:
How can Chronopolis be saved from alterations in time? I'm sorry to say, but that does sound like a novice fanfic thing that was made up for convenience more than anything else. If the altered past made Chronopolis built a mile away, and the one in the original timeline was immune to the past, would there suddenly be two chronopolises (I assume '-polis' is Greek so what's the plural?)?
How would Belthasar recognize Crono and co.? The only way he'd remember them is if he were the guru that they had to save on top of that mountain... and I don't remember if he was... He's not the same Belthasar that put his memory into the Nu and granted Crono and co. the Epoch
Why would everyone congratulate Crono and co. as heroes? I know that King Gaurdia welcomes them back at the end of CT as heroes, but he has to believe his own daughter, and he had the power to make a large celebration, but do you think everyone would suddenly believe that a group of teenagers saved the world when they have no proof? That'd be like if I told everyone here that I'd gone into the future and saved the world. I think that, rather than being praised as heroes, the crew should be marked as insane. Glenn had a high position in charge of the knights, or w/e, but I think his tales of time-traveling should be frowned upon (like everyone thinks he's talking about a dream when he talks about it, so they just ignore him when he does, and they pretend he's fine)
How is Belthasar able to communicate with the crew? Walkie-talkie that can send radio waves (are those what they use?) into the past? Yeah, right. I think it'd only make sense if he uses the Temporal Catch thing to take them into the future, talk to them, then send them back. Or, he could just go back and forth in time whenever he needs to talk to them.. However, whenever Belthasar talks with the crew I find it overly simplified. I'll find and post an example later, but it seems as if Belthasar talks and acts like he exists in the same time as Crono and co, but he doesn't. If King Zeal was erased from history, Belthasar should have no idea who he is. Also, he should be able to talk about stuff like "If I hadn't interfered with the past, you'd go here, but you'll walk into a trap if you do" or w/e...
I think that's all I have to say for now...