About the core eyes, there may still be a seeding bug with them making them too common. There was a forum post about this during the AVWW2 caused hiatus...
Anyways, about the Mk. IV and Mk. V stuff, there is a strong diminishing returns going on here.
Both the power and the m+c costs of the ships go up linearly with mark. However, the m+c slope is higher than the power slope (2x for the m+c past mk. I, but 1x for the power). This starts feeling really bad cost-effeciency wise once you get up to Mk. IV.
Plus, the sheer fact that it is a linear increase means that you are getting diminishing returns with each mark step up anyways. (Or more technically, for any linear function f(x), lim(x -> infinity, f(x+1)/f(x)) = 1)
I think this diminishing returns of power over mark is fine, but m+c costs and knowledge costs should be balanced somewhat accordingly (slightly higher than "fair" is fine, to keep pressure on late game unlocks high. But right now, its a bit too high).
I think something closer to the knowledge cost progression from Mk. II to Mk. III of the starships may be good for the fleet ships (IMO, the fleet ship costs should remain bit higher though) (this will help the adv factories)
Also, maybe reduce the m+c "slope" over mark (1.5x maybe? So you still are getting "less" for your money each mark, but not quite so punishingly)
(this will help both the adv factories AND the mk. V fabricators)
And finally, AIP plays into this. I would vote for making the "base" AI strength stronger (aka, the AI puts up more of a fight at low AIPs), but doesn't grow quite at strong as fast as AIP goes up (both the linear of <=8 and the exponential of >8). This should hopefully encourage people to be more willing to take stuff (both because they won't be punished for it quite so hard and because if they stay with low planet strats they will now be further behind due to the base strength increase)
However, the topic of AIP is big enough for its own forum post.