I think some of the weirdness with the campaign finances is due to mining worlds percent scaling and lack thereof for the Necrons. The Imperium needs the 100 a turn boost to get started, but eventually the forge worlds will generate as much as/more than a Necron crown world as you stack the mining worlds. I am only partway through my Necron campaign so it is possible that there are some mining world equivalents hiding somewhere I haven't seen, but I think the point stands. They give you the flat income on the planets to compete with mid/late Imperium numbers, but because you need to only upgrade that planet, and not a whole network of them you get that income much quicker while your fleets are still small and don't require massive expenditures. Which with help from the Dynastic Treasures, leads to resources glut.
In essence I think your right I never feel like I need to make any real tradeoffs because of resources in the Necron campaign like I did during the first 50ish turns of the Imperium Campaign (both on hard with gauge, just for reference).
@shaftoe That sounds like the battleplan transfer mechanics are bugged in the Beta. I never had any problems like that in the release version, and didn't see enough battleplans on flagships tonight to say one way or another in the Beta version, but if that starts happening I will be really frustrated too.
Problems 2-4 are really irritating to me as well, and I think the problem stems from the fact that the Admiral has the same level as his flagship, so you could just put a level 4 ship in a new admirals fleet, and instantly get the movement buff. So I think the first thing that needs to happen is to separate the Admiral's experience from his flagship, after all, an admiral is not the the ship's captain, and he doesn't forget how to command a fleet just because he is on a different ship.
After enacting this separation, transferring the ships and admirals around wouldn't allow you to game the experience system, and when this change was implemented there is an opportunity to give more control over the admiral's "load-out". Personally I waffle a bit on this one, I like looking through the different admirals and cooking up different fleet compositions to complement their abilities and upgrades, and then implementing different tactics with those fleets. Keeps the battles from getting too similar. But, I could still do that if I could change admirals skills around, so I guess that is a bit of a moot point. I think the admirals level should have more impact in general, maybe unlocking some of the upgrade/skill slots as they level up so you just can't grab a brand spanking new AdMech admiral give him Stasis Bomb and Disruption bomb (and five Nova cannons) and just go and annihilate a hivefleet while sipping his afternoon tea (or oil).
Problem 5 to me is really annoying as well, and I like your solution.
Problem 6 stems in part (I think) because the mechanics of the data recovery mission type from the last game are used, but never really explained. Once I realized this and remembered the rules, it became much more doable (not the same as easy or painless, but with less wtf happened). The first boarding action that lands (LS's are instant while boarding has a delay) transfers the plans to the ship that launched that action. The enemy however can get the battleplans back in exactly the same way, so once the plans are retrieved I move the ship out of boarding range, or warp it out all together. Sometimes I will use a LC for precisely this purpose: grab the plans with max range LS then burn for a safe spot/map edge and warp out.
There are also several systems that generate battleplans over time (which are finally working), which help a lot.
Now Problem 1, There are four standard Points of Interest (PoI) that generate flat resources (from least to greatest) Outpost, Civilized World, Hive World, Forge World. Outpost is so trivial that it takes ~20 turns to pay for itself at the start of the game (agri and mining world stacking reduce this considerably, later on). The other three are twice as efficient as the one before them 5/10/20 (CW), 10/20/40 (HW), and 20/40/80 (FW). You're right that in the early game (Pre-Agripinaa) you feel really income starved, I think that maybe they need to extend that first ten turn income buff a bit. But once you get Agripinaa under control most of the income problems ease up. In particularly the mining worlds in that sector with their percent multiplier really get things going. In my hard difficulty campaign I have the sectors Cadia, Nemisis Tessera, Belis Corona, and Agripinaa almost completely controlled and have roughly 5000 points worth of ships (spread over 11 fleets), which comes out to ~500 a turn upkeep, and am still making ~500 a turn. So a gross income of ~1000 a turn which feels like plenty to me,and it is going to jump once I take Reznor. Basically the economy for the Imperium snowballs due the interaction of its Forge/Hive worlds and its mining worlds. But I agree in the early bits of the campaign it can be a little rough, so I personally think a bit more of a starting economy buff would help.
Overall I think your points were well reasoned and well stated, and thanks for sharing them, and I hope you don't mind me giving my opinion on them.