My two cents on this is that the problem of everyone understanding some common language is too big to explain away. Language is an evolving entity and cannot possibly remain static. The growth of a language group across fourteen thousand years, let alone sixty-five million, would effectively mean different languages in different time periods. And yet, nearly all dialogue in the Chrono series is in some dialect of English. There are only two ways to interpret this glaring inconsistency:
1. Ignore the problem entirely as a part of the suspension of disbelief.
2. Pretend that each time period spoke different languages, and that Crono & Co. found some means to communicate with the people on various continents in each time period. Most likely that would mean adding length to the Chrono Trigger adventure as Our Heroes sought to overcome communication difficulties by learning a bit of the native language each time. For all we know, even places like Porre and Choras have different languages. If the El Nido archipelago can have as many different dialects as it does, then perhaps the entire Chrono world is a veritable jungle of competing tongues, just like our own.
For the purposes of playing the games, I recommend option number one. For any attempt at a novelization, I recommend option number two.
P.S. A third cent of mine, on the word "Zealian." The adjective is arbitrary. I call 'em "Zealish" myself, because I think Zealian is silly and Zealot gives the wrong impression. In any case, call 'em whatever you like, because this problem is independent of the much bigger common language problem.