I am currently designing a similar style game myself. The problems that you identified are complex and there are few solutions.

It would be very cool to have an ever expanding world where players each owned a part of the world and could customize it as they see fit.

One solution I came up with was to give each player a pocket plane that is only accessible via a gate of some kind. The gate would allow access to other players lands or it would allow them to access pvp or non-player controlled lands. This way players could create their world and still invite other players to their realm with little problems.

One thing you want to avoid is allowing players to build on one giant land mass since many areas would be poorly designed and managed. It would quickly become a place where no player would want to explore. There would be no lore or story to the world. The entire world wouldn't appear to be believable since it would look like the building sprawl of your typical RTS game where buildings are haphazardly placed on the landscape.

Another problem exists with players who don't play very much and their lands become inactive. If they are part of the greater landmass then you can bet that most of your neighbors will be linked to dead accounts. This will especially be the case if you limit the number lands that can be controlled by a player. You could allow the natural environment to take the land mass over (returning it to the wild or something), but even then the world wouldn't be believable.

My resolution for inactive accounts is a self-solving one, in that people are always able to attack other peoples territory, the difference is that with no-one present to defend it, it will just quickly be swallowed up by neighbours.

Having influence over a region doesn't really DO that much for a player. It gives them more of a free reign (and possibly the ability to charge tolls and fees for its use) than over the wilds.

There is no great fence between people near each other, nor are they forced to have any land at all. It's just another method of playing the game (which is primarily a run around and either zap/slash/stab people and creatures.

It's hard to remember what I need to write here when I have it all written down in notes all over my desk. But yeah, this territory control is just another feature. Whilst it may be useful to claim dominion over a large section of land, it is by no means necessary.

As for avoiding the haphazard placement of structures and the like, because the territory is really not THAT big of an issue, it won't affect the viewport all that much (Think cities/ZOC in CivIII, except the cities would be cheap 'markers'). Players will eventually be able to construct up to 3 buildings on their land (A house or rest area, an NPC controlled shop, and an outpost) this is a non issue. Players marks left on their land will mainly consist of taking its resources, not permanently changing it.

Current plan for a map is to have a friend design a land mass. Players will be able to claim territory nearly everywhere. There will be some restrictions but not many. My solution to players claiming important areas would be to encourage player policing of it. In games where big or old players are claiming large territories, making many small enemies is very dangerous, and I'll be working to ensure that this is the case.