You mean aside from how layered the time travel centred plot was (something that makes Primer look like a Disney film), the complicated subject matter (the deepest elements of the philosophy of space and time (such as the relativity of simultaneity and the causation solution)), the complicated nature behind the order in which the story presents itself, events that connect together in unexpected but thematically appropriate ways, the sheer dimensions of thought that the story deals in etc etc.
You yourself stated that Moby Dick, one of the all time great novels, was only more complex that Chrono Trigger in areas where it didn't deal with time travel. Well Chrono Trigger is a time travel centric story, that is ultimately what the story is about, and it tells a time travel story as complex as any other with the exception of the other two games in its series.
If all of your area of "complexity" have to do with time travel then you've already ceded the point without realizing it. You are not even over-analyzing Chrono Trigger: you are attributing to it things which it does not have. The question of the philosophy of space and time was in no way introduced or even alluded to in Chrono Trigger; the ramifications of killing Lavos was the intent of neither Kitase nor Matsui, and trying to pretend otherwise is to parade about with a lie. More, bringing up that they worked out an internally coherent system for time travel does not make the whole thing any more complex than The Terminator and its various incarnations, it just means that it has time travel. Time travel is not and cannot be equated with narrative complexity or depth. "Sheer dimension of thought the story deals in" is a meaningless phrase that you're reaching for because you can't actually touch on a single point of narrative complexity in this game outside of perhaps Magus's relationship with his family - a point I would have conceded, but you have let it slip by and it is lost to you now. "Events that connected together in unexpected but thematically appropriate ways" is a similarly meaningless phrase in this context, because you can't actually name a theme that Chrono Trigger is supposed to have.
Chrono Trigger's story functions becauase it does not pretend to complexity. It's a Dragon Quest game.
Again, you are confusing "complexity of plot" with "complexity of narrative"; the former is only the barest sliver of the latter, and even if Chrono Trigger was as big a mess as you're making it out to be (it is not) it would not actually be complex in a narrative sense. Any given chapter in Moby Dick - any chapter - involves far more symbolous ruminations about man and nature and the universe than the entirety of Chrono Trigger, all of it woven into the narative so easily that most people will never know it's there.
I feel like I'm insulting Melville by making the comparison. It's ludicrous.
Worse yet than your equation of complexity of plot and complexity of narrative is your equation of complexity of narrative with quality of narrative, which you have failed to actually substantiate in any way.