Waygates as opposed to teleportation
Instead of instant teleportation, how about Wheel of Time type Waygates for faster travel. this could be really cool because it could implement the "other dimension" quality of Arcanus and Myrorr from MoM, but instead of an entire other plane it could jsut be a method of quick travel.
So you could access "the Ways" thru random towers scattered around the landscape. Towers would initially be guarded by fairly powerful creatures so they couldnt be used for zerg rushes, you would have to defeat the guardian before you could use them. You would also have to defeat the guardian at the exit point if it had never been beaten. Alternatively, players might have armies guarding the tower so your force might be ambushed - better send a scout ahead to see what's waiting!
I don't think there should be a whole other plane with cities and resources, that would be too much of a MoM rip off. But say there were relatively narrow paths to the different towers and while there your units either had 3 to 4 times the travel ability OR the path from one gate to another was much shorter than over land. There could be choke points and crossroads that being able to hold these positions in the Ways could be as important as holding other resources in the main map.
Maybe there should be detrimental effect for a unit that stayed in the Ways too long, so setting up a permanent stronghold and thus controlling travel indefinitely would be extremely difficult. Maybe have some spells available that you could either summon creatures that did not suffer from the effects, or buffs you could put on units that would either temporarily or permantnely protect them from those weakening effects.