I played a lot of Full Thrust and can heartily recommend that. It is however a classic game with the administartion that entails. If you don't mind checking boxes, the game is fantastic and basically miniature agnostic, although it does have its own fluff. Ship design is possible. It is a Capital ship game, with swarms of fighters operating as a unit. I don't think it had aliens IIRC.
Silent Death is also very good, designed to play on a hex map but can be converted to tabletop with simple tools. It is basically a fighter game, with only the smallest of capital ships. Very entertaining. Also classic in terms of bookkeeping. Ship design is possible. It has a strong Alien faction, the Night Brood.
Star Wars Armada is also a superb Capital ship game, with many similarities to (but a LOT more depth than) X-Wing. It has a very influencial meta game, which you can see as an advantage or a disadvantage depending on your taste. It s (of course) also limited to the SW universe and needs its own range of miniatures. The SW canon is, of course, crawling with aliens.