(SPOILER)1. He fell through a time gate with nothing but the clothes on his back. He had access to his own magic, which is completely pitiful and only does anything when he manages to get your party with a "look over there" move. He had access to zero technology and magic outside of that, and he had little brains, having stolen the Blackbird and the Epoch, rather than developed anything himself.
2. Golems. That's about it.
3. Except... You face armies. You wipe the floor with Magus's army, remember? Or what about the Robot armies in the future? You know, the ones about seven times more powerful than Dalton's cronies, yet you can still annihilate with a single spell?
4. Both being inferior in power to Lavos, and therefore not enough of a balance tipper to upset anything.
Even worse, however, is that the game doesn't even attempt to handle this issue. It makes no explanation, the characters have no appearance or presence in the game at all. It just goes "Yeah, this stuff happened. Deal with it, and please don't ask why these incredibly powerful, important people are never ever going to be seen during the entire plot".
It feels like the developers were intimidated by Chrono Trigger. Like they felt that actually using anything from that game might be seen as ruining it by their fans, and cause an outcry. As a result they handled everything from Chrono Trigger with a fifty foot pole. And because of that, the entire thing feels really, really weird. It's a sequel that's afraid to be a sequel. It's too scared to actually step up to the role it was given, and so it can never do more than sit in the shadow of a much better game.
Chrono Cross exists in limbo, unsure if it wants to be a sequel, a spin-off, or a new world. Its references to Chrono Trigger are poorly handled and minimalistic. And yet the two games are still tied closely enough together that Chrono Cross's flaws are also measured and judged by Chrono Trigger's, a comparison that will always leave Chrono Cross wanting.
And that is why I think Chrono Cross is better enjoyed on its own. Because, while it does have some gaps and missing backstory, taken as its own game, it has to stand on its own, and can do so. Taken together with Chrono Trigger, it is a toddler standing for the first time, unsure if it needs its parent's help or not.
Although, again, none of this matters, because regardless of the best way to play Chrono Cross, the best decision for anyone who hasn't played Chrono Trigger yet is to GO PLAY IT NOW. As in, immediately.