Brain is also an accomplished inventor. He's invented all sorts of Rube Goldberg-esque machines in his quest for global domination. Though my favorite invention of his was the allergy powder he made to sneak into Fort Knox.
Also remember that, while Pinky does act as a foil for the Brain, Stewie's diminutive size are constantly doing the same for him. (Remember the episode where he wanted to buy that huge machine to enslave the human race at auction, but couldn't because he was so short no one could see him?)
Also notice that his objectives are to kill Lois and then enslave the world. As yet, Stewie has been utterly incapable of the matricide he so desperately wishes to achieve. Personally, I think Brain will have taken over the world before Stewie even comes close to offing his mom.
Additionally, bear in mind that Stewie's delusions of grandeur almost always backfire - instead of speeding up time with his time machine (to skip teething), he rewinds and his machine gets trounced; instead of killing off all the broccoli with his weather device, he managed to just fall off the roof; and let's not forget that this is the same kid who blew himself up with a box of active grenades.
Plus, I think the Brain has the experience on Stewie here. He's learned a lot of lessons (the hard way) and, assuming he's able to learn from them, this should be no problem at all.
Suffice it to say, I voted for Pinky & the Brain.
