I actually enjoy the RTS, warts and all, but a lot of people don't. In many cases the complaints are too many units on the field to control.
I see too many posts of people basically saying that they stopped going to RTS and just auto-resolved Act 3, which is a shame because it's a really fun challenge to deal with in RTS mode.
I've played custom campaigns with changed rules, and they play out much differently.
In the Beta, one of the things we requested to try was making strategy map units more useful in the RTS mode. Larian did notice and one patch was an experiment to try to do something about that, although what that test actually did was to make strategy map units even LESS useful than they were before before reverting it back. Larian didn't try increasing the costs of units in RTS mode, although they did add these options in for the custom campaign settings.
I think that adding a "Custom" difficulty setting to the Story campaign that lets you change some of the rules might encourage at least some people to give it another chance.