This spoiler is focused around things you learn in both the Dinocity quest thing, and the bonus dungeon available the second playthrough.
(SPOILER)First off, I think that the Dino city has something to do with Dinopolis in Cross. In part because I think the Idea of you saving the civilization that causes you so much pain later on in cross to be hilarious.

The second dungeon, however, answers a few questions in cross. First off, how did porre become a powerful military nation? The answer is simple. Remember how Dalton was sucked into the protal after attempting to summon the Golem boss? Turns out he got lost in a dimension vortex and found his way to your home time. Using the magic of Zeal, and likely technology from the future, he managed to turn porre into a military state and conquere Guardia, all out of spite for you beating him.

The actual ending I believe ties more into the alternate Radical dreamers universe then to Chrono Cross.

Feel free to correct me on my ideas though.