I fully support the idea of giving things a contemporary settings, minus political themes.
When you finish Chrono Chross (the good way), Kid is shown searching through a modern day city, walking along railroad tracks, etc, looking for Serge. In the grand scheme of things, it's pretty random, sure, but I like the idea of game with a more modern settings alongside the time travel theme (because obviously you'll be headed back to the days of swords and magic anyways).
Look at a current game like The Secret World. Granted, it has nothing to do with time travel, but it's an RPG in a modern setting with a very interesting story focused on impossible, supernatural events in a modern setting. It's not all ghosts and spooky creatures either, it's full of almost alien entities, such as the filth, a corrupting, pervasive creature full of disease that spreads its sickness to everything it touches. Not that I'm suggesting we copy anything about it (besides it's setting, which isn't saying much), but I think it's a great game to look at for reference.
Also, through all this talk, I haven't heard anything about an antagonist. Trigger had Lavos. Cross had Lynx (and Fate). If this new game is simply... battling time, and event/s that will or have happened, it's gonna be really vague and unimpressive. We need a really, really, really terrible antagonist. We knew we HAD to defeat Lavos. He was gonna eat the damn world! We WANTED to kill Lynx. We watched him kill Kid's family! We need a similar creature to hate in this game. Beyond that, I think we need a strong, dark individual with motives of spreading something extremely dangerous through the world. He SUCCEEDS at this, and we see the devastation he's wrought. Without copying TSW's filth creature, I think it would be a powerful, scary element for this antagonist to spread a similar, infectious blight of death and disease across the world, corrupting all it comes in contact with. It would be a pretty grand undertaking, especially if this enemy could traverse time periods, leading to very tense encounters.
Anyways, just brainstorming, but we definitely need a good antagonist.