Not to mention the super-commandos, who are an elite variant of the regular Mando commandos. While CIS commando droids are effective, the Mandalorian commandos have an edge due to expansive training of the Mandalorians vs. programming. While programming may be advance, it cannot necessarily replace the hardcore training of the Mandalorians.
While the CIS fleet was quite large and quite strong, the Mandalorians blocked the Hydian Way (which couldn't be broken by the Republic) until a smuggling cartel assisted the Republic in breaking it. Keep in mind that Hylo Visz was a well-experienced pilot and cunning in general. The CIS fleet was strong, but could still be brought down by the Mandalorians cunning tactics. Here's where the Mandalorian commandos come in again. If the commandos can sneak on board the CIS ships, they could destroy the ship without a large threat looming over them.
All in all, I'd give it to the Mandalorians due to their extravagent tactics and the factor of the commandos and supercommandos
I think people are starting to over-state the importance of special forces. The super-commandos are not going to win the war for Mandalore. They can't destroy one ship at a time or undermine one world's support at a time. There are thousands of both of those.
We have to remember, this is an entire GALAXY. Special Forces do not work as they do on our Earth. The only way tiny Special Forces will make a sizable impact is is they go for the top.
Speaking of cunning tactics.... The CIS was able to make it to Coruscant. What's to stop them from doing the same with Mandalore (the planet)?
(Ok, last post for a couple days! Help me, Grievous supporters!)