There's a few things with this...
Crono is sent by Guardia in the first place. He eventually comes upon Alex and saves him. I suppose afterwards Alex could kill Guardia... we'll see how it works in as the plot develops.
I like the idea of fighting a "special battle" at the end of the game. I don't know if you should really fight Frog / Glenn and Cyrus or Serge or anyone like that though. It doesn't make as much sense. Glenn and especially Cyrus are long since dead, and Serge... well in 1005 AD I think he's been either just created or born or whatever.
There will be a new game+ and in it you'll get to start from other characters perspectives. I'm thinking you can have a Vera game and the girl that you rescue, etc. You can also start another Alex / Crono game of course. I think at the present moment though, you can only choose up to 4 answers in a multiple choice scenario... but I'm sure I can fix that easily enough, in fact I know I can
The demon lord... is this going to be Alex after all, or is it someone or something completely different? If Alex does go mad.. I dunno, we'll see.
I think Crono dying (again) will or should be expected. But I think it should be like an end of game scenario if that does happen. You have to remember, there's going to be multiple endings for multiple characters... hence many dimensions... hence trying to delve into a very deep, complex, and complete story... I know how to do it, it'll just take time to develop plot and such.
I'm also not sure why Magus / Janus and Schala / Kid would be at Crono's grave. I can definitely see Kid as Kid there, with Lucca. Lucca saying something like, accept the future or something. Quote the letter she sent to Kid in Chrono Cross. That would make more sense.
Not bad over all though. It should be interesting to see the many different perspectives and / or directions this story can take us.