For my taste, this game would be perfect if I could auto-resolve those fights that happen randomly while traveling between cities.
I know I can lower their strenght and ocurance, but thats not exactly what I'm looking for. I just do not like arcade element in them (when I have to give orders by clikcking and all that hasty-hasty stuff) but I do not mind making sure I hire enought of a crew to defend and manage relations with enemies.

I guess thtas not possible in current game (or is it?), but is there any chance for that kind of change / option in the future?

Yes too, I find those arcade games feeble, even they are not so numerous.
( I think you actually talk about the arcades, and not real time tacticle battles that we can pause )