Firstly, this 'CPU' you are talking about was made using Robo, so their villain is some one who, at the very least, should be considered on par with any one member of the party. Of course, the moment you make this concession it's no longer anywhere near the lopsided fight you seem to be implying. So this CPU could realistically have the knowledge of how to take advantage of Crono and Marle.

I think a safe assumption as well is Daltons entire contribution to this ploy, mind you, was supplying the arsenal. I mighty arsenal it may have been, but it is still Dalton. For the most part I think we can assume it's Crono and Marle Vs. Fate/Lynx.

And it's also silly to say Lynx lost to some boy from a fisher village. Not only because Crono too was just some guy, yet he managed to overcome incredible odds. And also, mind you, he got his ass smoked by Lavos in solo combat.

Next, fighting a single enemy, no matter how powerful, is an entirely different matter then fighting an army. Mind you an army armed with trout none of your troops could possibly be prepared for, and backed up by Fate itself. Take into account Crono and Marle, much in contrast to the previous fights you mentioned, didn't have to worry about other people getting killed in their battles.

Also take into account Fates control over the world, which while not absolute is something Crono not only has no way to prepare for, but is a massive advantage for team evil here.

Don't get me wrong, It would be nice to have a lot of these details fleshed out and explained, but at the same time all that game would be doing is filling out minor plot points, and not really adding anything to the overall plot and questions of Chrono Cross and triggers continuity.

Maybe a short, not full price game would serve best.

I do agree that a lot of this was pulled out of their ass, but in the end I don't think it creates as many problems as you seem to think it does. We are given plenty of reason to see just why Lynx and Fate are such formidable foes.