There are plenty of things we can turn off in the game to prevent them from making things ugly or cross-eyed. Shields, engines, deflector dishes, kits and personal armor can all be visually disabled in order to prevent them from fouling our experience.
Please give us the option to choose which postion the long range science vessel's silly flipper pylons are in. There are combinations of nacelles and pylons that look good in either the up or down position but look all derpy once the ship wiggles its flippers to the other position. I can't see any good reason why there can't be a context menu with "auto flipper", "flippers up" and "flippers down" can't be added onto the ship so that it can have a satisfying look (to its captain) at all times.
That would be nice.
But I'm still waiting for them to put on the 4 missing navigation lights on the fan-tail and blinking running lights on the saucer and hull.
Like, 10 minutes worth of copy and paste work ~_~