First off, great review. I agree with 99% (1% margin of error) of what you said, so I'm just gonna go through and explain some of the reasonings behind why things were as they were, and whether or not any of it has been fixed yet. (Not that it makes it any better that they were that way. There was just a reason.)
Before I say anything else I would like to apologize for the wait. A number of unexpected planetary invasions pushed back the finishing of this review by about two weeks. I was ashamed.
No mod team ever has the right to make anyone apologize for keeping them waiting.

-While I understand replacing the planets with asteroid like polygons saves a few ticks of the CPU I found that it largely took away from the ‘feel’ of dominating the universe. For example, when I destroy Endor and I see this lush gree and blue world turn into asteroids and planetoids I get a sense of satisfaction knowing I have just obliterated the tribes of furry Ewoks and millions of species of plant life, yet when I turn this one brown polygon into the same brown polygon I don’t feel like a mass murder at all. =(
Agreed. This minimod had a lot of experimental stuff in it, so we did that to see just how much we could reduce lag on the galactic map. This solution not only looked like shit, but it didn't quite improve the speed as much as we hoped, so it has long since been removed.
-I found that Borleous, Fresia, Garos IV, Anaxes and Coruscan’t are too close and I have trouble moving fleets around between those planets.
This was partly due to rushing. Since then I've made the galactic map bigger, the planets smaller and zoomed in on the map, so those kind of proximity issues no longer exist.
-Borleals, Garos IV, Mechis III, Chandrila, Helska 4, Ando Prime and Karick all have some problems either with missing text, missing tooltips, missing descriptions, missing abilities, or missing ability icons.
Forgot to do those for the minimod, being fixed.
-On a few of the new planets I have noticed that you can’t see your base garrison when you first capture it.
Pretty sure that this was a problem with EaW and has been fixed in FoC....
Planet Abilities:
-Anaxes and Xa Fel’s abilities don’t stack.
-Garos IV’s ability doesn’t work because you can’t build an imperial research facility on the planet for some reason or another.
-Corulag’s ability doesn’t affect rebel medics, or Imperial Guards.
-Wayland’s ability doesn’t affect the T3-B tank as it’s description would lead you to believe.
The issue here was lack of communication. The person who was in charge of doing the text didn't bother informing the person doing the planet abilities what abilities they were, so they weren't always properly implemented.
Land Units:
-The At-St is no longer buildable in tech 1 as the ‘tech tree’ would have you believe.
-The L-1 tank occasionally appears all black.
-The light armor upgrades from Endor and Land Tactical battles don’t apply to the new lightly armored vehicles. (Tie Crawler and the L-1)
-Carnor Jax: Force push ability mentions Darth Vader.
-The Empire’s “Tech 4 Upgrade” mentions a ‘Repulsorlift Jammer’ that is no where to be found.
-T-2b tanks unstoppable early game…
Tech tree issue: don't know how to edit it, if you can at all. The AT-ST was moved to tech two as the AT-PT was in the minimod until pretty much the day of release, this is also probably why the T2-Bs are hard to kill early game, as we haven't touched them. Repulsorlift Jammer was Petroglyph, and was cut before they released the game. That text has always been there, we just didn't remove it.
Space Units:
-Strike-Class: no pop value shown.
-Mc40a: when the shields are destroyed a large chunk of an ISD bridge appears and falls off. Humorous.
-Quasar Fire-class: the description doesn’t say how many fighters they hold, assumed limitless.
-The ISD1 and ISD2 are buildable in the same tech; there isn’t much reason to build an ISD1 other than lack of money.
All fixed, except ISD1 and ISD2. We may move ISD1 to tech four, but they now have very different armaments. Just ask me on skype, and I can give them to you.
Miscellaneous:
-Random crash to desktop when combining fleets.
-The ‘Droid Log’ page makes reference to a mining colony planet ability that doesn’t ever appear.
-Some of the new land and space maps are really too big, takes 20 min. to find the enemy. Also, they lack the build pads that put an end to the T-2b rush.
-Unlimited garrisons make planetary assaults buggy, in terms of finding rebels still on your planet after you take control of it.
The CTD was also an error with EaW I think, haven't encountered it since moving to FoC. Droid Log text hadn't been edited, so same issue as repulsorlift jammer. The space and land maps will remain the same size, as sometimes you need that much space to be able to win as the Rebellion or with small forces. However, field commanders are now able to reveal the entire map. Not entirely sure what you mean by the garrison thing.
Finally, welcome to the team, you deserve it....