(Be nice to the newbie, please forgive any mistakes/things that I didn't notice.)
Be glad you said that

1)Planets/Asteroids with Odd logistic slots
Its part of the upgrade process -- you can upgrade logistics and tactical, so that the number of slots increases. The final logistics slots (with the maximum number of upgrades) is always even ATM. (Edit: This was covered in the tutorials, I believe)
3) Odd AI
Its a beta

Devs are focusing more on gameplay and engine stability (aka: bugs and *gross* balance issues) rather than AI ATM (though AI is still being worked on, from what I understand).
5)Fighter-Bomber "immunity"
Flak frigates can hit fighters, and thats what they're there for

6)Auto-auto placement
There's an auto-place button just to the right of the little photo thing of the unit you have selected. It controls whether auto-place is on or off for most buildings (in options, you can also choose auto-place always on for metal and crystal extractors, a must IMO). (Edit: And I think this was covered in the tutorial, too

)
I was always rather surprised when I looked down and I saw the planet counter and I said "Oh, cool, I didn't actually notice that before, huh, weird." and then quickly forgetting it existed. Point being, perhaps there should be something of more importance at the bottom of the UI, as to cause the player look at the whole screen.
Those items are actually context-sensitive, carrying different information when you have different units selected. For example, if you choose a ship its HP, shields, and anti-matter are displayed. Also, the little "news-cards" to the left of the photo are
immensely helpful. Not only do they sort incoming events into four logs, and then let you examine each event log separately, by clicking on them you can browse through the recent events (and go "back" with R click, forward with L click).
I don't know if this counts as part of the user interface, but I would really like to be able to change/customize my insignia.
You can do that at the start of the game. IIRC, you control your icon on the same screen as you set your name. Colors are controled at the screen where you set-up your opposing players, however (wierd system, I know). Maybe the devs should make it a little easier, by making the color controls for the player be in the same place as the icon controls, then simply "locking" the chosen color out when changing the AI's color.