I have 2 main PoV's, one is a question and one, an idea.
1st thing:
How exactly will this play out, are there mountains separating it, hit an invisible wall (god no...please), or can you ACTUALLY get inside their territory but then guards start spawning in until you are overwhelmed (the longer you stay the bigger the guard number). Im one of those that think this is not exactly a good idea, but hey, we haven't seen the game yet, so i'll just stay skeptic instead of full on against it.
Also as a separate thought, how much territory does each faction control? Is it like, EVERY SINGLE LAND is owned by each faction and only cyrodil is the grey area?
Or are there specific "capital" lands, and then provinces which CAN be attacked, if so, then it does make sense to have locked out "capital" lands, if not, the idea explained below might appeal to some.
The other thing is, it could have strategical value to be allowed to enter the enemy territory.
Now im not sure how much overpowered it would be, allowing sneaky characters to come up and then start casting fire spells burning everything up (50 guys doing it won't be a pleasent experience for the guys leveling in that area). But for example allowing certain amount of ppl to group up and do some skirmish should be available, like killing off some npc's that are known quest givers, since everything you do in the game helps the war effort, it would allow underplayed factions to still be a threat, but this is also a pandora's box, if the said faction employs these tactics too much, it might anger the rest of the 2 factions and then they will simply invade them in a "hidden alliance" of sort.
A way to prevent large scale battles occuring on enemy grounds and allow only small, fast paces, short duration skirmishes would be a small guard army coming to intercept the invading force, and they should be extremely tough to beat if not, invincible (infinite soldier replacement), and their numbers should grow more and more until the threat is gone.
Now I know most of you who heard about the game will say, there are already fort attacks, and whatnot, but it would be nice to hurt a bit the enemy heart as well and not only the lands in cyrodil.