@admins: removing the admin cost for colony ships would help - colonization is already limited by pop growth anyway. Of course, then the Colonizers trait and Admin Center must be removed or changed. Alternately make the Admin center available for everyone (easily done: just remove the perclusion section). If possible, scaling the admin bonus from citizens (slightly) with galaxy size divided by numbr of players could help, but I suspect once colonization is fixed, that's not as much of an issue any more.
@resources: I don't know how the scaling is right now, but it seems that, currently, when you leave the galaxy settings for resources alone, and only change galaxy size, the relative abundance of resources does not scale linearly with galaxy size. IMHO it should, but I have no idea whether it's possible to handle this via XML. That said, the greater issue is that the amount of resources needed, especially for some late game modules and buildings, is too high. Also some of the resource types are used for too many different purposes at once. I may have felt it more than other players because I play synthetic: in very large galaxies they can't keep up with other races pop growth due to lack of durantium and prometium needed for pop assembly. And then there's no resources left for the many other uses. Just to make a point: in my current game at around turn 100 I spent a lot of effort to build or trade for all durantium mining starbases. But even with ~18 Durantium and ~15 Prometium per turn, that's still not a lot of growth I can achieve for 100+ planets.
Maybe it would help if synthetic and silicon races could unlock advanced methods of pop assembly later in the game, that require less resources per unit of pop.
@tourism: the problem is it's linear scaling with ZoI which grows too much in large galaxies. Tying it to number of planets would be better, or maybe making the relation to ZoI sublinear (e.g. square root?).
@research: should be scaled with #planets divided by #players
@citizens: empire wide bonus should scale by #players / #planets, otherwise there would be no point assigning them to a planet.