(1) In several space battles with the New Republic, the new intruder (forgot name) occasionally jumps in and fights everyone. Several times, when the New Republic is on the offensive and they retreat, the battle ends, eventhough the new intruder has not been defeated. I vaguely remember this being discussed in the past, but could not be fixed.
That's how it's intended to work (or at least, has to work within the game).
(2) After defeating the Imperial Remanant on Bilbringi (there were 4 Golans in space), I built 3 Golans, but on the planet view there are only 2 boxes with Golans, and the small text on the top left only shows two types. In addition, the boxes show 2 Golan IIs, but the text states Golan II and Golan III. Also, on the space build UI, the Golans are still shown as buildable. Can I build more than 2?
You can build as many as the planet lets you build. The boxes cannot be expanded to show more than two, the text at the top is meant to display everything on the planet, but there may have been a bug if you didn't see all of your stations. We're exploring different ways to display them, but that would likely be beyond 2.2.
(3) Starting week 41, for space battles, my frame rate has noticeable dropped. Nothing has changed, but the week. Is this worth pursuing?
The week wouldn't have any impact on the framerate. It may be that you're coming across different types of ships in different frequencies that have more or less strain on your system.
(4) On several of the base layout maps, e.g. Anx Minor, the location of units, buildings and placement positions are not shown. If this can be fixed, I can include a detailed list. I vaguely remember this being addressed years ago.
These are automatically generated by the map editor. When the map is saved again by the editor, it overwrites the data and has to be extracted, so we will once again have to go through and get it to re-extract. It is, quite frankly, one of the most tedious things in the fucking world and easy to go wrong without noticing because there's really no indication of how well it worked until you come across the planet (one of 240) ingame. In any case, for 2.2 we've cut most of our own maps and reintroduced most of the vanilla maps, so we'll likely have to redo it for all of the maps which are staying anyway.
(5) To help a relatively old guy, is there some way I can lighten the blue color for the Penstar Alignment to make it easier to read?
2.2 has brightened all of the colours a bit, but this can be found in the Expansion_Factions.xml. If you search for the "Pentastar" section, in the first bit of code there's a set of RGB values- you just plug in the appropriate values for whatever colour you like (if you don't have photoshop, then the internet is full of decent RGB viewers)