I just put in about 4 hours, and here are some things I noticed:
1. Rotation of gravity well graphic when zommed on a ship is disorienting as it feels like the ship is moving sideways sometimes. Perhaps a 'pulse' every few seconds to make it feel futuristic/tech-ish would be better.
2. It would be nice to have an auto-fighter mode that would launch fighters when attacking, and dock them when not fighting. To take it a step further, it would be nice to have some mechanism whereby they avoid anti-fighter ships by themselves -- this is a wishlist item, not so much a suggestion, though.
3. When you order a ship to jump, it docks the fighters. If you cancel the jump, the fighters will finish docking. Not a big deal, just not sure if that's what you intended.
4. When pausing a game during the playing of the phase jump spin up sound, the sound will play through twice, then stop until the game is un-paused, then play again. Another minor detail.
5. Fighters seem to be happy to fly through planets to get places more quickly.

Wonderful game. Keep up the good work!