It was Larian's intention to allow players to ignore using RTS combat in favour of auto-resolving if they wanted to. There's already a lot of complaints about the RTS mode, can you imagine how much louder those would be if RTS combat was mandatory?
If you want to play RTS mode instead of auto-resolving, then do it.
Again, I like the idea of giving you the option of selecting what forces you bring into the battle. Unfortunately, I don't think we'll be seeing anything like that unless there's a Dragon Commander 2.
