First off, I am extremely happy with the engine and am eagerly awaiting February.

Here are my nit-picks

Phase Shift Animations - When facing a phase shifting ship head-on, one notices that nearly all the effects are one sided, looking very poor at that angle (could just be my GFX settings). Also, when zooming between Planetary and Galaxy views, the animations for a few ships occasionally disappears.
Phase Sifting Ships - If grouped and told to group move, they do not always phase shift together, more often than not half will phase shift, and then the other half will phase shift.
Path Finding - My Building Frigates sometimes feel it is necessary to go over my Planet to build a structure, when it is the exact same distance to go around the planet on the horizontal plane. When navigating my Colony Ships around a Star, they do not go around the Star like one would expect, but rather attempt to go straight to its destination and grinding up against the Star's collision sphere (not the Star itself).
Pirates! - As stated by many people, they will periodically attack me with forces far too large for the defending Planet's defenses. While this is smart in theory, it is often that all of my forces are on the other side of the map.
Tax Rates - They are just a tiny bit too slow/small, not by much though.
Engine Trails - They are drawn in proportion to the engine port. This creates extremely short engine trails, which render many nonexistent and difficult to tell if your ship is moving if zoomed in.
Edge of Screen Pan - An option to disable edge of screen pan would be nice.
Graphics Menu - Titles for each category (resolution, refresh rate, etc.) should be there, and they clearly are not.

Overall I am extremely happy with the game, only small things here and there need to be tweaked.