I saw this video the other day and thought it was good:
Every problem he has brought up I have already tried to compensate for in my design. The main problem he doesn't see around I solved by removing completely. In a standard RTS game you build a base to make units, I removed the base. My system has large scale factions (large teams of players) who all pull together to make the bases and earn bonuses from those bases existing. The player then is left to control his units and feed resources to the bases.
With unit upgrades, my design downplays in favor of stronger/more advanced units. I then balance those with unit slots limited players to how many of those units can be used; you can you a lot of small guys, or a few large guys. That gives the younger players still a fighting chance to band together and help the battle. For example, if you use a "warrior" and a newbie uses a "warrior" those two units will be about the same (there is a veteran system so it isn't exactly equal). However the higher level player could have 100s of these warriors while the newbie would only have a few. The newbie can either level up and get more, get better units, or find several friends. These 20 newbies each with 10 warriors would be more than a match for the higher level player. More likely the higher level player wouldn't have 100s of warriors, (s)he would have fewer "Elite warriors" which would be harder to kill, but don't bring the sheer numbers of units to the field.
At the end of the episode, this ExtraCredit guy starts to take the MMO out of the MMORTS. He cites 4 vs. 4 battles to help a larger economy, but that just ignores the massiveness.
By the way, the "End of Nations" he mentioned at the very end was cancelled. This is why I feel I'm on the right path and can turn this into something big. The market wants it, I just need to do it better.