Yes, several of the events become more interesting in Proportions, because things take more effort to build up. A couple of times I've found myself doing all I can to evacuate populations with large fleets of transports.
The maintenance costs is a good idea and I'm glad it works. I agree that military installations should cost maintenance, although it will need to be balanced carefully and tested to see what good values are. In the early game there is an abundance of resources, but fleet maintenance is already pretty expensive. If facilities cost too much, it might be really hard to make much net forward progress at all. Take your game a bit further into the "mid game," and see if you're able to develop a helpful infrastructure.
Another neat thing might be to make pre-arcology urban developments consume more organics than they produce.
Have you been using fleets of transports to increase build rates? Cities can take forever if you don't, but if you can get enough population, then they become more practical investments. Of course, if you have enemies, those parades of transports should probably be guarded...
PvK