Thanks neozeks. Personally I thought I'd started rambling, but there you go
I think I actually lean towards the indirect option. The direct option would be more democratic but considering just how huge and diverse the Federation and it's population are, the difficulties of campaigning and voting also seem quite huge. Computers and advanced communications could solve the problem, though.
The other interesting point to make about this option is that it doesn't require other planetary governments to be democratic. Since presumably they can send whoever they want to the Federation Council as their representatives, an indirect system would mean that on a non-democratic planet operating on a feudal system, for example (like the Klingons), they could send representatives from their High Council (if they ever joined the Federation) without having democracy 'forced' upon them. It seems more in line with the Federation's policies on inclusion.
Energy, land and means of transportation are still finite though. I'd imagine that while everyone still freely gets enough credits (there was this site that had a nice, detailed theory on this) for comfortable living (sufficient housing, enough energy for replicating most stuff you need, ordinary transportation needs, medical coverage), you still have to earn, by working or saving, additional credits for more luxury stuff like a really beautiful house on a very good location, buying a more-energy-demanding or handmade object (didn't Scotty buy a boat?), a trip to the other side of the Federation and such.
That's true. We've heard mention of 'transporter credits'. Perhaps for other 'top bracket' items there are still requirements, call them credits if you will, which might even be determined by prestige (of a person's job, or their achievements) and there'd be a finite number. Perhaps there'd be some form of barter exchange or the ability to save them up. Not calling it 'money' sidesteps the fact that Earth supposedly doesn't use 'money' but still limits what are otherwise, as you say, finite resources. Not everyone can have a big house in the country, after all.
Trek isn't quite post-scarcity in the same way Iain M. Bank's "Culture" is, as you rightly say there are still apparent limits on land use and potentially top dollar luxury items.