Ironhide is ill-suited as a leader on a covert mission like what the Autobots were doing on Earth. He's very good at direct combat tactics and achieving a decisive victory, but not very good at leading missions that require subterfuge and guile.
I don't know if Ratchet's much better though. Remember that Ratchet was in agreement with Ironhide when it came to "offing" Sam's parents for being highly annoying. Ratchet doesn't seem to have displayed much in battle initiative or charisma in the movie - merely following the directions of others.
I think that Jazz would be a good candidate if he hadn't been killed by Megatron as Jazz does show good charismatic initiative. Jazz led the Autobot counteroffensive against Devastator ("Decepticon punk!") and also led the defensive manoeuvres against Megatron; which is where Jazz fell in the line of duty. Had Jazz survived I think that he would've been a good replacement for Prime. And besides, he's next in rank anyway. d:
agreed :P where's sari and her allspark key....
You jest, but give Mikaela something phallic like an All Spark Key to hold and watch the teenage (and adult) guys drool even more!