Thoughts so far:
* Subatomic Simulators are almost always worthless, due to the very low base science production. Spending 80 Energy for 20% local science is usually a net loss, even discounting the expense of building the thing. This gets worse as tech increases.
* I'm not sure if growth rates have to do with the faction chosen or with the luck of the map. Growth seems fine as Klingons, Cardassians and Federation, but Romulan growth seemed very low.
* Someone really loves Klingons! Their ships are reasonably priced, have low maintenance and pack a devastating punch. A big fleet with first turn cloak advantage can wipe out an equivalently sized enemy in two turns with minimal losses; their ships are a bit less attractive before cloaks come online (All 6). The Targ Hunting Preserve at level 2 is both the cheapest and earliest available morale structure, and its food to energy ratio makes it worth turning on. The gulag comes a bit late at level 6, and only provides a modest Industry bonus which is not useful everywhere, but more Industry is always welcome; its -1 Morale is irrelevant because the Klingons uniquely get a +2 Morale structure! Klingon Intel production is a bit low, but Science is fine (with Weapons and Energy boosters too!) and Industry is great. Colony ships are expensive, however. After getting used to Klingons being the worst in BoP, maybe this is their rightful time to rule the roost.
* Cardassians seem well-suited for spreading trash across the galaxy. Their ships are cheap but meh. State rations are useful for getting a colony off the ground quickly at low tech levels, but isn't so great a building once Colony II ships are available. One meh morale structure at Tech 6 gives the Cardassians the worst morale setup in the game. The Obsidian Order provides a morale penalty, and the Cardassians get nothing special to offset that.
* The AI seems to have a big problem playing as Dominion. Their Dominion always seems much smaller, weaker and less advanced than other AI factions. Maybe this is because their Industry, Science and Intel all suck, and because their ships compensate for being crazy expensive with fragile defense and inaccurate offense. Their unique buildings are mostly "who cares." I'll try the Dominion at some point to see if I'm missing something, though the stats seem to tell the story (and I miss the Ferengi voice acting.)
* The Federation seems solid. Private Farms come early but less than Targs and more expensive. The unique Federation Science building is perhaps the best single (main faction) building in the game. Best science but worst intel. Most worlds don't need much industry, so a local building that provides +80% at key production systems is reasonable. Morale not as good as Klingons, but second best is fine. Tough ships.
* Need to try Romulans again. I started a game late at night, and their growth rate seemed horrible. Bad luck with nearby systems? Me too tired to pay attention? Weird that Klingon and Cardassian science is no worse that Romulan science for the first few tech levels (with Klingon science being better due to better morale; Targs are good brain food!) Cloaking from the start is nice, and having many long-range, accurate torpedoes also nice. Organic Regenerators are a waste of space.
* Morale situation: Structures that provide morale without power are better; Klingons get the best of these and Dominion the worst (not even worth powering!) Everyone except the Dominion gets a structure that provides Morale when powered; Romulans gets the best of these because it comes earliest. As always, Feds get the most morale for being friends and get penalties for being naughty, but they can now bomb with impunity. Even with minors in play, I suspect Klingons>Fed.
* Unlike BoP (but very much like vanilla), building ships to target tech jumps is very much a thing. For most factions, the only offensive ship worth building before All-8 is the 4-level command ship, keeping an eye toward accumulating a fleet just before the jump to Command Ship II at Almost-All 6. This is especially true of the Klingons, for whom this is the first ship to cloak. Romulans and maybe Dominion have an interest in Strike Cruisers, due to their advantages with Torps, but SC Is are too slow to be useful. Each faction relying mostly on one class of ship is pretty typical across all BotF; it might be interesting to reconsider the main ship types to make Fast and Strike ships more useful (say, by making them all cost the same but playing with accuracy, defenses and so on, rather than by treating small ships as cheaper but less effective; this might be realistic, but that realism doesn't work in a game that doesn't support the (also realistic) idea that 100 small craft can patrol and control an area but 1 battleship cannot.) It might also be interesting to see a mod in which ship costs go *down* as Tech increases, while Industrial output remains flatter; fleets do seem to get much bigger over time during TNG and DS9, though that's more about our technology than theirs.
* BoP nerfed weapons, causing cloak to be less effective and (I think) planetary bombardment to be less effective too. I suspect cloak is once again especially awesome. More play is needed.
* As usual, the AI does not know what to do about rapid human expansion on a 40*30 map. I suspect that the AI imposes less pressure here than in BoP, which is strange because AI fleets are bigger when I first encounter them in UM. In both cases, I do feel cautious about having enough ships and especially Intel to defend as my rapid growth brings me into contact, but whereas I fear an early encounter with Cardassians or Romulans in BoP before I have Intel build up, or with anyone before I have a decent navy (especially playing Cardassians who get the worst ships in BoP), I don't quite feel that here if I can reach All-4 before my first AI encounter. Doing so seems quite straightforward, so building a warship beforehand seems silly.
* The BotF system Production Screen UI starts having problems at Population 400, because the little slivers representing 10pop get sliverier and sliverier. They are harder to count and harder to manipulate. UM features huge systems, exacerbating this problem. (I wonder whether halving pop and pop growth but doubling per-pop output would work. Or quartering. A small 50-pop system being the equivalent of a 200 pop system is less fine-grained, but also involves less mm.)
* Unlike in BoP, troop transports actually have enough troops to do something other than die horribly (after all that expensive maintenance as they slowly move toward their target.)
* I continue to like the simplified, no upgrade structures. This does change a few things: Morale and other local % bonuses become less important, because the base is lower. Industry becomes less important, because most systems need only enough to churn out 110/turn, and even those can be vacated sooner than in other mods. A new science or intel structure on a new world is about as effective as one on a big, developed system, making it much easier to quickly ramp science or intel.
* As usual, I found myself turning off minor races. I love meeting them, and love the idea of them. But it remains so easy to acquire a minor race early in the game, even as a non-diplomatic faction, and minors are even huger and better than ever before, some with incredibly fast growth rates. If you have a 1000pop and 2 700pop minor on Turn 60 or so, you're pretty much set. (And conquest is much easier here than in BoP.)