Updated and amended:
Ideology Issues
1) Mindfulness says it applies to "your first 3 worlds," but it actually seems to apply to many more... all 20 of my planets in a current game have the mindfulness bonus.
2) Pragmatism is adding the Gross Income bonus but not the Research bonus.
3) Some options don't subtract points when unlocked. So far, I've found this to be true of Empathy, Pragmatism, Prominence, Beacon, and Affinity.
Rally Point Issues
1a) You can send ships beyond their range using rally points.
1b) You can send constructors beyond their range and build star bases.
2) When you open the shipyard "Set Shipyard Destination" screen, sometimes the "Rally Points" tab doesn't work. It seems to consistently not work when you first open the screen and attempt to click that tab first. If you click any of the other tabs, you can then select "Rally Points." When you select the "Rally Points" tab and it doesn't work, you hear an audible *click* and the word is highlighted as if it is selected (shown below), but the filter is not applied.

Visual Issues
1) When zoomed in past the tactical view, ships sometimes "vibrate" when moving, and around corners, they show up for a frame or two pointed in different directions.
2) Upon reload, trade route paths still don't display properly. They are quite annoying.

3) Planet images in the right-hand planet screen seem to display at varying sizes still.

4) Still lots of text display issues inside tool tips, in Galactic Events, and in Colonization Events.

5) Two of Age of War manufacturing specialization techs don't display properly:

6) When you select Research Project, the research production figures on the planet don't change unless you move either the production wheel or the manufacturing/shipyard slider.
7) Similar to #6, if you adjust the planet's production, the changes are not reflected in the manufacturing queue until you either add something to the queue or reopen the planet screen.
8) What is "Raw Research" and why does there seem to be no equivalent in manufacturing? In manufacturing, everything seems to be percentage modifiers (though what is being modified isn't clear in the tool tips--it should be). But in research and in income, there are "raw" or "gross" figures, respectively. What determines these figures? The tool tips are lacking here as there is no indication of where the base numbers originate--they are present (because the manufacturing percentages are obviously modifying something), but they are not being displayed or explained.
Ship Designer Issues
1) Components no longer remain selected after being placed. In Beta 1, you could set a component to a certain size, rotation, etc. and place multiple. Now, you have to reconfigure each repeated component one by one. This is tedious.
Mechanics Issues
1) When the manufacturing queue is empty, please make it so all manufacturing automatically goes to any connected shipyard. Right now, the only solution is to manually set the slider to 100% shipyard, but then if an upgrade becomes available, you have to manually reset the slider or change every planet's production using the global reset...