1. more double/triple techs. but with a catch: instead of collecting points to get the next PRESET tech, you choose between two, like marle can choose between attack magic and healing magic, chrono can choose physical tech or sky tech, etc. while we're at it, a different leveling system where you're credited for what you DO in battles, like if you attack a lot you get strength and speed, if you heal a lot, you get magic and hp, if you defend or use items, you get evade and defense. something like that. would make pvp possible, would be more like cross's system(which i thoroughly enjoyed, a departure from the norm) and would cement the idea that you control your own future.
2. more dinosaurs in prehistory. you get dactyls and trex's. but there's so much room for more. seriouslythis game has everything else. (say this out loud really fast) robots, mutants, TIME TRAVEL, apocalyptic future, magic users, a DEVIL ALIEN, swords, knights, tanks, explosions, epic landscapes, FLOATING ISLANDS, people with radically unnatural hair colors, monsters INSTEAD of animals (domesticated not included), magic badguys who EVOLVED FROM SAID MONSTERS, causality, humor, tragedy, dragons, giant frogs, cavemen, castles, human sacrifice, the END of the WORLD, dino people, friggin dracula(either magus or slash, take your pick), and A COUPLE DINOSAURS. i say MORE.
3. bigger towns. it felt weird going from huge dungeon to huge forest to huge factory to tiny world map with a couple buildings and each one has one or two people in it. it felt epic because along with the story, there were a lot of eras to visit, but the world itself felt tiny. especially when you compare it with cross, which i find overpopulated and hardly magical. it needed more dimensions to go to! that's all i'm saying. maybe fewer characters. at least ct's few characters are pretty much all bad-asses.
4. am i the only person who wanted to physically change frog to his human form? or see it happen, even in an ending, or a fast underdeveloped cutscene, or a quick explanation of how he gets to be himself again? cause i saw the psx ending and i'm not satisfied at all. that may be an imposter as far as i'm concerned. they don't show his face. they don't show him change. i think noble tragic hero frog is hiding in his forest house and eating worms cause they found fake glenn. i hoped they'd add it to the psx version in-game. i hoped they might do it when i heard about the ds version. no dice so far.
anyway, that's pretty much what i would change.