DC-17m rounds could do a lot against MJOLNIR armor. He has the regular blaster rounds, sniper rounds, and an anti-armor grenade. An EC grenade would take care of his shield (And with several EC grenades he could keep the shield down for a good, long time) so he wouldn't have the benefit of its protection. In Republic Commando, I believe when a Commando is in the radius of an EC, it stuns him temporarily; a similar effect could perhaps be expected on a Spartan. I think this has less to do with the armor and more to do with the natural electrical impulses of the body being scrambled by the grenade.
Also, a vibroblade (From what I have read) can cut through solid rock. Something with that amount of power could easily do a lot of damage in certain key points (Neck, knee, elbow, shoulder, waist) where there are weaker joints in the armor to allow movement. The entire suit isn't made of titanium, then the Spartan wouldn't be able to move. I would assume the material covering the joints is similar to kevlar, which wouldn't be able to stand up to a vibroblade. The Spartan still has the advantage in close combat, but the Commando could still prove a challenge (Vibroblade through the neck, for instance).
And for your last comment... SURGE PROTECTERS! Heck lets face it, if you had to create a super soldiers armor, chances are it would have at least something to keep it from over loading.
Using that logic, they would also be equipped with fire extinguishers (In case the systems overloaded and caught fire), a wench hook-up system (In case he got stuck in some mud), a built-in virtual library in his HUD (In case he was on the pot with nothing to read), et cetera. You can't prepare for every possible scenario, it's just not cost-effective. Those suits are already costing an ungodly fortune to make, proofing them against things like electric charges and such would only make it worse (And impede the soldier). Plus, when the Covenant doesn't use those kinds of tactics, why bother? If you go to play a baseball game, you don't bring boxing gloves because you've spent a lot of time and money training, and you don't want to lose a game if the other team randomly decides to box instead of bat.
Know what I mean?