Few things:
First - Heroes! Make them all recruitable on WOTR map.
Second - Heroes! Same thing, but with CaH.
Third - Dwarves! There's only Erebor, which is available in WOTR. It should be changed somehow.
Fourth - Two battalions which are given at the beginning of each skimrish you play in real-time mode. They should be disabled.
Fith - More slots for players in WOTR? I know, it's propably not possible, but that would be great to put into one game all factions (Gondor, Rohan, Arnor, Imladris, Lothlorien/Mirkwood, Ered Luin, Erebor, Iron Hills, all Misty mountains factions, Mordor, Isengard and Angmar on one map!) try to imagine this!
And last, it's like dwarves issue - Arnor! It should be available. Maybe it can depend on starting position? If you start on Arnor teritory, you play as it, same with Gondor and Dwarves factions.
PS. if Dwarves can't be done, just add heroes and units from Ered Luin and Iron Hills to WOTR mode. (not all heroes of course, only the ones whos alive during War of the Ring time.