I sign on, and poof, there's a new version, so some of my comments are a bit out of date, but here's my list
General Stuff
a) I'd like to see some carryover in the missions. Some tech, some planetary development, some ships -- even though I might lose my favorite survey ship in mission 3

For example, for each scenario set the starting tech at one level, and the maximum allowed techs at a later level. This opens the door to a new mission, one where everyone has the same tech, and there is no tech development. The goal could be to secure some important resources needed to break through to the next level of technology.

The Altairians frequently told me they were joining me against the Korx, and the Korx often told me they were attacking me to protect their Torian allies, despite the fact we were all at war.
c) In the War missions, the UP can declare a cease fire!
d) The game isn't remembering my username and email addy on the screen at the end. Perhaps if I play a real game, and submit it, it'll save it
e) The end of campaign scores don't always line up with the camp/miss/new total
f) I somehow lost the cumulative score during mission 6, so at the end I was at 0. Check (l) below for a guess as to what did it.
g) In one of the team vs team missions, the Altairans built Diplos. As a result, they thought me barbaric, and wouldn't trade. I ended up restarting that mission, heh.
h) As noted earlier, restarting a mission with new picks is not easy.
i) The second autosave isn't properly named
j) When saving a game, a list of games to save over is no longer generated. (just noticed they're back in latest version)
k) Once the Altairans are Teammates, doesn't seem to matter if I turn evil.
l) Checking through the scenarios, the minors are supposed to be off. This is a good, I think. In one of the missions, after loading from the improperly named previous autosave, I think a couple minors popped up. I bet that's when I lost my cumulative score too.
Mission Specific
Mission 1: Currently, new storyline info can only pop up at the beginning and the end of the mission. Mission 1 should really start with Admiral Rabid Rob taking command of one of Terra's new colonies in the deeps of space. We have detected signals coming from here and here, please investigate and make friendly contact if possible, if not, secure the quadrant from aggressors. Later, when I meet the Altairans, and then the Korx, then new info should appear.
Mission 2: I think this mission should also require an Alliance with the Altairans. This would also be a way to control the level of technology as the missions progress.
Mission 3: The Excalibur is really fast, and can see everywhere on the map. The second thing bothers me the most, but that's built into the AI I think... Perhaps put a beacon on the Excalibur so we could see it in return? I'd classify this as a more advanced scenario, it should be later in the sequence, since the difficulty should gradually build. Actually, though, I was quite amused by this scenario, since I ended up flooding space with sensor probes and frieghters to keep the Excalibur distracted while I sent Transports and Star fighters way around to grab the planet. Woot!
Mission 4: Oh, were those Drengin? This mission would work better if both the Drengin and Arceans were a fair bit advantaged over the humans. This is also a good time to build up the galactic background story.
Mission 5: Since all the resources were Over There, this led to a very interesting development in my war. I put up 1 starbase, cranked up its defense and offensive bonuses, and then proceeded to kill the Korx with my ampped Corvettes. LOL
Mission 6: This map is too small. It's very easy to just charge in and take their planets.
Mission 7: I hate to think what would happen with the high level Influence penalties if anyone else grabs the center.
Mission 8: Starting in the same square scared me, I immediately restarted at a lower level. We didn't flip each other with Influence, if we don't have to worry about teammate influence, that should be mentioned somewhere. If it is something that has to be worried about, this mission is evil incarnate at higher levels
Mission 9: The end is a bit shocking. Suddenly all these other empires are mentioned, and the background story of the galaxy pops in from nowhere. Having news bulletins pop up about developments in the far corners of the galaxy during previous missions would create a larger, galactic atmosphere. To add to the fun, draw up a picture of the galaxy, with Sol clearly marked (add more later as the galaxy developes, eg, Terran space expands and Altairian space shows up when they Team with us). Draw a little square on the galaxy pic, and do a traditional "exploded view" to the mission area map.
/essay
It's too bad the Korx won't give me a chance to help them, muhahaha!
A good start, with hints of more to come!
~SDC~