You know how the bad luck rolls with those mk IV's...and the first wave still has the small wave rule.
What small wave rule?
Lots of good ideas here. And it would be just randomly game breaking to drop a +80 effective AIP for waves next to a human homeworld. In much the same way that dropping a raid engine there would kinda be mapgen saying "gg". So a wave-size-increaser would get similar seeding logic (3 or 4 hops out, I forget how much), and probably still be optional, yea.
As far as making other AI structures redundant like armor boosting... there should be enough variety that it doesn't happen very often, but if it happens it's not a big deal: redundant != useless; you might raid an armor booster more or less at-will, but you'd probably think twice about spending 20 AIP to take an armor-boosting-command-station down.