I definitely liked private galaxies in the early rounds. I think they should be able to join an alliance as a whole (otherwise some will just be out of tag) but there should be no alliance travel time benefits to private galaxy users.
Alliances (without private galaxies?) get several other benefits that don't count for priv gals, such as "Alliance Status" - and BP up to 3 people for random gals. Add all that to the alliance ETA bonus they get and that the priv gals don't get, and I think you might have a fair balance between galaxies and alliances, and it would make joining random gals more interesting for larger alliances since they rely on their alliance and not just their galaxy for def. Ally cap of 60 players should probably be upheld then, or perhaps even lowered. Cluster def eta bonus should be upheld too, even for private galaxies, but put both private and random gals together in a cluster, and maybe make clusters smaller. (up to 5 galaxies per cluster)
Private galaxies will then be forced to work with their clusters and themselves for def since the only benefit they have from joining an alliance would be maybe attacking. Alliances will have a good counter vs galaxies, and galaxies and clusters could even declare war on alliances (why not?)
I can imagine a bunch of hardcore players take the challenge to win the round solo. But it also means that random galaxies will actually have a real use for their GC, MoD, MoW, and MoC.
Only problem I can really think of is cluster alliances interfering with regular alliances, as in forming huge blockes. Perhaps the cluster def ETA bonus should die if you tag up, for both random and private galaxies. You already have the alliance eta for random gals, and private gals will have their own defensive core, while private galaxies who don't tag can get cluster def.
Might be worth a try.
Private galaxy should be up to around, hmm, I'd say 7 to 10 planets, with random galaxies being around 15.
Just theorising here, using a lot of the ideas already suggested
