Freelancer sorta comes into mind... I haven't played Zone of the Enders, but I do remember kinda what it looks like. Freelancer is more of a fast paced arcade-space combat type game with plenty of laser weapons and missiles. The game is a little on the older side (I think 2003ish) but has graphics that will hold up to today's standards and I think it still has a pretty good modding community with plenty of mods to suit the game to your style. It does have plenty cut-scenes, descent story, and simulation elements (like upgrading your ship, trading, and whatnot) and, iirc, you can't skip the cut-scenes, so I'm not sure the interruption of combat/gameplay is what you wanted. It's definitely worth a try though.
This post makes me want to re-install the game
