There were several ships and technologies available to the New Republic BEFORE their research in the tech tree. Assault Frigates start out constructable, despite not being researched. Force Pull and Force Push both have research points in the tech tree, but both abilities are available without doing the research, and neither research seems to unlock anything. Are these researches simply to improve the ships or abilities in question, or are they supposed to be unlocking things?
I've just checked the Assault Frigate and it definitely requires the research to build it.
As for the Force Push/Pull thing, with abilities there's two separate tags to tie them to research; I'm pretty sure Pali is correct in that you can spec it but can't use it but I'll check, and we'll likely use both tags in the future to prevent confusion.
I liked the split between civil and military stations. One thing, though: When playing multiplayer, will teamed players with disgusting amounts of money will be able to construct stations over each others' planets, as in base Sins? If so, it's still possible to get all the station benefits on one planet: simply build civilian stations over your own planet (for the government-in-orbit, max-allegiance-increase, and trade), and military stations over your ally's planets (to actually blow stuff up). If you trust your ally (or have locked teams), then you get all the station benefits over your most important planets.
I don't think there's anything you can do to prevent people from building them outside their own territory. That's also how people control uncolonizeable gravity wells though too, so if we could it's probably not desirable.
Our ships were defecting left and right to the enemy NR factions, which kinda sucked.
Don't get me wrong, I love that passive (10% chance for ships to defect when they leave your gravity well), as it forces the enemy to engage you one planet at a time. But when strategy demands a lightning strike deep in enemy territory, it's just too damn powerful a defense to overcome. Even three planets in and it can strip an invader of half their fleet. Great when they're defecting to me; awful when my ships defect to someone else.
Can Fleet Commander auras be made to lessen the defection chance?
There are a lot of values in the mod that are pretty overtuned just to test functionality pre-1.0, and this is probably one of the worst offenders. When it's finalized, it's likely to be around 2%. That being said, while it would be nice to have the number be alterabl;e by other factors, it's determined by a flat rate in research that cannot be changed or influenced by anything else.
Just signed up to leave some feedback, figured I'd add it in here. 
Currently playing my first .95 game, and just had a couple thoughts on the UI. For the planet UI, I love having the type of planet show even when zoomed out, though currently with no colony techs needed, it doesn't really matter. However, I also have something I don't like, and that is the ship indicators for friendly and enemy ships. The circles are always there, so unlike vanilla, it's not that easy to tell if there are ships at any given planet. I know it fills in red depending on number of ships, but if you only have a couple ships at a planet, it's hard to tell is something is there. I'd suggest that you only have those indicators appear if there is a ship or enemy ship at the planet like the fleet indicators in vanilla.
It does still work the same as vanilla; the indicators only appear with ships, but the casing (in vanilla the brackets, in the mod the circles) are always there. That can't be changed. We will however look at decreasing the thickness/intensity of the side circles so the emphasis is more on the coloured bits.
After further play: The NR Endurance fleet carrier needs a serious tweak during balancing, it loses a massive amount of firepower compared to the Nebula to carry only 1 more squadron than a Quasar. If it's keeping the current sad firepower numbers, it should field at least 6 squadrons of fighters. As it is, I see no reason to build it at all, it's got no firepower and not enough fighters to even really call it a carrier. You're far better off building 3 Nebulas, you get the same fighters and massively more direct firepower.
As Pali said, the abilities have a large impact in this case, and it's a great support ship; rather similar to how I think people undervalue the World Devastaor next to the Praetor. 6 squadrons is vastly more than anything else in the game and gets way too close to the fighter lag problems that make the game unplayable, and when considering fighters it's important to keep in mind not just the amount you can field at once, but also sustainability. Between fielding one extra squadron at a time, two extra squadrons over a battle, and the buffs those fighters get, it's significantly more powerful. The other thing we're looking at doing is making fighter counts scale up with levels with dedicated carriers. That being said, it is getting some combat buffs (not enough to bring it anywhere near the Nebula, but there was a typo that took away a significant portion of its damage).
Oh btw, the captcha for signing up/posting is a bit much, wouldn't you say? I feel for any dyslexics trying to sign up. 
It's an unfortunate necessity until better spam prevention becomes available; it may seem excessive, but immediately after any of them are removed the forums get inundated with (no exaggeration) up to 500 spam accounts and 100 spam posts per day.
Don't know if it's on purpose, but unclaimed planets always seem to be protected by 2 carracks or one lancer or one lance and a carrack. I kind of miss having to work at all to colonize better planets even if they are just neutral. Makes larger games a bit tedious before you actually run into your opponents.
This is one of the major things in 1.0; populating the maps with more pre-set stuff, including neutral stations, fleets where they make sense, and other stuff.