The glaring issue is interface problems and cut corners that are frankly inexcusable.
Example #1: Some planets have special features that can be quite significant. The initial tutorial message advises you to read up on any specials you encounter in exploring. Sounds like a good idea. First check the in-game 'Encyclopedia'. Keyword searches for 'planet specials', 'specials', 'storms', etc all come up empty. Revealing that the Encyclopedias contents are pitifully limited and even so the keyword search feature is aggrevatingly weak. Try the manual--the manual which has blank pages for notes but no index, for which somebody deserves to be fired (probably a cost-cutter somewhere). Nothing to be found. Eventually it becomes clear, you get to see the effects of a special on the colony screen--in other words, it's a big mystery until after you land there. Great!
Example #2: "Spies have destroyed a Govenment building on Ilias" "The people are afraid, we need to do something about the spies" Great. Well, good luck finding the Espionage controls, and when you do, what kind of spy do you need? Well, there doesn't seem to be any counter-espionage task. Would extra ground forces help? Who knows? Finally I turned up one line in the lovely unindexed manual--"Boosting the oppressometer will give you a little protection against enemy spies, but it will raise your unrest too." From turn say 20 to turn say 70 in a medium difficulty game, I couldn't keep a goverment building constructed for more than 2 turns before a spy destroyed it. And that left the world (my homeworld) largely crippled. Fun!
Example #3: The interface is horrible. In terms of functionality it ignores well established usage standards--eg it's annoyingly hard to de-select ships--right clicking to de-select doesn't work, [Esc] just brings up the Exit Game dialog. The layout is clearly designed for looks rather than effective information communication. Symbols are used without being a link to a definiton or having a 'tool-tip' explanation. Important information is buried offscreen in scrolling or collapsing areas while large areas are sparsely populated by numbers you'll hardly ever look at. Similarly, tech advances are described in text blobs when of course almost all of them could, if anyone cared about usability, be first described with a one-liner and the details to follow for those interested.
Basically this game gets a D on usability, which is a failing that is really hard to overlook when you're on the 3rd installement of a series in a now well populated genre.
Given how long they've been working on this, and the obviously large potential of such an anticipated game, it is shocking that they couldn't find anyone competant to address such things. (well, less shocking in the aftermath of the last Pool of Radiance game, I guess)
For similar reasons, the shortage of graphics is disappointing. I don't mean I need Mechwarrior 3 (or was it 4)style effect-overload in menus. But there are 14 ship sizes and only something like 6 graphics. Even worse for bases--14 sizes and only 3 graphics. These aren't complicated models, and a little differentiation and scaling to fill out the spectrum would have been less than a week's work for one person--easily.
So it's got a lot of problems. I'm sticking with it, I want to see more. But part of it is, I'm afraid, I'm trying to learn from its mistakes.
A couple years ago they were talking about having only a limited number of actions per turn. That sounded promising to me, given my fond recollections of Star Control 1. If the human and the computer opponant are limited in the number of actions they can take, then the human's ability to prioritize by feel offsets the machine-speed analysis of the opponant. I wish they'd stuck with that. The planetary viceroys help, and the turns go by pretty fast at the outset. I get bogged down not by having a lot of things to do, but rather trying to get one or two things done in the unwieldy interface.
The combat is pretty bad so far too. I was a fan of MOO1 for combat. Less simmy, but more fun to play. Perhaps they wanted to get away from players being able to win tactically with inferior tech or numbers. Well, they did, and it stinks for those like me who suffered through the empire management for the thrill of commanding an important battle and winning with wacky tactics. Combat is VERY hands off. More appealing than Rebellion so far--but less appealing than MOO1, MOO2, IG1, IG2, SE4, etc.