Actually, the CIS eliminated that key flaw. After the failure at Naboo, the Trade Federation enhanced the Droid Armies to allow them to operate without the need for a Droid Control Ship. As it stands now, the Lucrehulk-class Battleship no longer acts as a Droid Control ship. It now serves as a blockade vessel and transport ship armed to the teeth with heavy firepower. It is capable of carrying over 100,000 droids and almost 7,000 AATs.
I feel that almost everything that needs to be said here has been said. The Mandos just don't have the numbers, industry, or Jedi that the Republic had while fighting the CIS. They will lose.
However I'd like to make a point concerning the droid army: look at how what happened at Naboo. Droid armies always have that all-important generator. Once it is down, the army is useless. It can't be TOO hard to shut down a army of droids, after all: a small fighter squad was able to do that. We need to consider if/how Mando strike teams could do such a thing. Regardless, I'm sure this will take an effect on the battle somehow.
Also: if/when these droids are shut down, would it be possible for the Mandos to re-program these droids? I don't know if the Mandos are capable of such a thing, but if they could pull this off, it'd make a difference.
If the Mandos can do what I just suggested then they'll make it an interesting fight, but I'm afraid they'll still lose the war. In the end, it won't be a landslide win for the Greivous, but it won't be close either.