I always play regroup, because I find it more fun, more challenging, and much more in tune thematically with the developers' original conception of the game. That being said, the one thing I hate about regroup is that all of your ships disappear at the end of Antiquity, and there is nothing at all you can do about that. Historically, I can't think of a good reason why that has to happen.
So just as army commanders influence how many military units carry over into Exploration, I'd like to see some way for naval units to carry over as well. This wouldn't necessary need to be in terms of some sort of Antiquity age fleet commander. Something as simple as letting one naval unit carry over into Exploration for each harbor you have built would be just fine with me. As things stand now, I resist building any naval units at all during Antiquity unless they are absolutely necessary, and that feels very bad to me. Especially since, as others have mentioned here, barbarian ships seem to be more prevalent and more aggressive in TOT, and so ships of your own are more often needed to ward them off.