The point is you said 'No, they never intended to be a Chrono Trigger sequel', while they did. Kato just wanted to create a game that is seemingly unrelated, having the connections very deep. I'm wager he's foreseen there'll be CC haters like Jonny here. Making a different sequel doesn't mean the same characters go through new adventures on another planet.
Crono: 'wowz, we r flying in space and fighting lavos! i 8 lavos, gawr! lol'
Marle: 'crono don't die i love u and if u die lavos sux lol'
Lucca: 'lavos planet! crash!'
Seriously, Kato does something I think more developers should do: When they have a good game, they don't just keep punching the formula and milking it for more cash and fanbase, but rather changing the formula while developing the story to expose the game for a different fanbase. It's better to have sci-fi fans then just plain nerds who keep saying 'magus ruxxerz major suxerz'. He took a brave risk, a risk more people should make. He made the plot an even greater work of genius, and idiots who bash it piss me off like hell.