The main culprit here has got to be the single player game. The AI in a mission can be challenging simply because it's been designed specifically for that mission. In most cases the AI has a pre built base with lots of units and defences, and is set up to usually only react to triggers. In addition, you may also have them behave the way we would want them to when you take control. We've already seen how the bots in the FPS games have improved in a relatively short period of time, I'm sure the same could be done for this genre.
Balance is the other big one.
The balance in RTS games has been pretty solid for a number of years now. One thing that the developers must always keep in mind when creating a balance, is how a change will affect both sides of the game. A change made to help fix a hole in the multiplayer game could very easily make a mission completely unbalanced. To get around this, sometimes a change will only take effect in the place where there is an issue. However, then you have the problem of getting a slightly different game when you switch back and forth from single and multi.