Ultimately I don't think the problem is the current system, or the players who are active within it. I think, often, that there are IC responses to problems like these. I think many players who have complained about being unable to get a shop in high-traffic areas, for example, haven't tried contacting the shop owners in an effort to arrange a purchase or trade, or to sell goods in that shop with the owner taking a percentage, or sent assassins and thugs after that shop owner, etc. Checking every day to see if a high-traffic shop has come up for sale is not a viable strategy and will just leave you frustrated. In low-traffic areas that sure can work, but never in high-traffic spots.
While characters who have deeply entrenched themselves in their various holdings aren't just going to let them go, I suspect that if you RP with them and try to figure out a way to get involved, most of those players will be happy to work with you and make some kind of deal. Or you can force their hand by sending thugs or assassins after them, blackmailing them, etc. There are a number of options to take.
If you don't like a faction owning a bunch of mansions of empty rooms instead of using just one guildhouse - great! Then go to the settlement leader and explain your position. Post on boards decrying their opulence and denounce them as fat lazy thieves that don't help the community. *Join* the faction and make change from within. I can think of a dozen different ways to put pressure on a faction or character that does something like that, and most of them are particularly effective on 'good' characters that practice differently than they preach

As others have pointed out, I think the problem is inactive players doing pseudo-acceptable things like quarterlogging and trading properties/valuables/shops OOC. Whether it's intended maliciously or not (see AstralUniverse's post a couple up), that's the sort of behaviour that makes Arelith suffer. Tragically we are human beings, and as such there will *always* be people who skirt the rules for the benefit of themselves and their friends (see: all of history).
We can't reasonably expect a small team of volunteer DMs to constantly be watching every player. And it's impossible for them to know what sort of communication is going on OOC. I can only echo what Mattamue and some others have said: if you see quarterlogging, shoplogging, obvious OOC communication, or other poor behaviour, report it to the DMs. Help them have eyes on rulebreakers, because they're the ones who can deal with it.