Though I belive you see all the problems better than me I'll make a list of
distance balanses.
The pirates is ok but could be closer. Will three be any other city in the desert?
Mordor is fine
Minas Thirith is way to close if you want Osgiliath in the game.
Dol Amroth is ok, but they could get an outpost closer to the rest of gondor to get them more involved.
Rohan is to small. Will there be any Edoras? In that case they need much more space uppwards. Helms Deep (and Minas Tirith) will need space compared to the unit collision size.
Dunland is good.
Fanghorn is maybe a bit close to Isengard. If you just melt it together with Lorien there should be lotas of space.
Mirkwood is huge and takes a long time to travel through. Therefore Rhun will use to much time moving his forces.
Will it be any rhovanion? And will you fill wastelands with neutral enemies?
Should be it. It is possible to fix the current map, or make a new one. Anyway it would be lots of work.