In the end, it all comes down to us asuming this wild speculation and a few bits and pieces of evidence that aren't even solid and could easily be just co-incidence (or however u spell it ^_^).
And Crono and Marle may have seperated and parted in their ways to hide across the globe. Think about it. Marle could have gone into hiding way over in Choras or some small island way out to sea. Crono, the stronger and wiser one, goes to El Nido, where all the action is happening, he changes his name while at it, and takes his daughter with him.
And with the 'ghosts' or watever they are, i belive they are mere projections of the three time travellers minds, at this point in the game, they may have all been dead, communicating together in the after-life. And the reason they look young is because its for the gamers!! The gamers know that the time travellers are young, not looking different, its for us to recognize!!
~I could be wrong though...