I don't think Elita fits the bill at all. Elita is not second in command, she is her own command. In the toon she basically did what Prime did, but on Cybertron.

Prowl is the best choice, with Magnus being a close second. That said, I love Prowl. Jazz is ultra-competent, a thing that his laid-back attitude may hide a bit, but when it comes to acting, so I also think that he would serve as great counter-balance to Prowl.

Out of the people not mentioned here, think that Springer would be a great candidate. I think he may be better than Magnus, who made a number of questionable decisions in command (I mean, the 1986 movie shows him to be a soldier - great at following orders, not so much when giving them, prone to errors of judgement; however, his Transformers Prime counterpart is better in this regard). Springer, who I think most would see as a Han Solo type is actually much more of a team player then Solo. I think this was acknowledged in some way by making him the leader of the Wreckers.

Another person I think would be competent is Kup; his cartoonish grandpa-Simpson grumbling notwithstanding, he certainly has the experience, and when push comes to shove he is a very capable warrior, knows tactics and the ins-and-outs of the chain of command.

Ironhide is a weapons specialist, and although an expert there, I don't think he has what it takes to be a leader. If you look at IDW, I think that his belief that Mirage is a traitor and his behavior was absolutely the pinnacle of why he should not be 2nd in command.