Cena would absolutely be the top guy. People constantly overrate Brock Lesnar's impact on the business--mainly because of the huge affect he had had in UFC. But in WWE, he honestly didn't really move business terribly much. And let's not forget that his one babyface run flopped because he was so boringly one-dimensional in that role.
Cena as an upper midcarder in 2004, at the time pushed at a fraction of the ferocity Vince pushed Lesnar, was responsible for more than 1/5th of WWE's merchandise sales if I have my numbers right.
I see no reason at all why Cena would not have jumped over Lesnar pretty easily if Lesnar had stayed around. And here's the funny part: while Batista may not have received the kind of push he did if Lesnar had stuck around (whose absence impacted the pushes for JBL and Orton before Batista), if they had pushed Batista just like they did in his defiant face turn against Triple H in very early 2005, it's pretty clear that Batista would have surpassed Lesnar, too, if all things remained equal. Batista and Cena were responsible for creating something of a "mini-boom," so to speak. Merchandise sales, ratings, gates all went up as they were pushed to the top and anointed. Batista was Raw's powerhouse draw for the first half of the year and when he migrated to Smackdown, their business went up, too.
By comparison, Lesnar's impact on business throughout his two-year run was very marginal. He was a very good foil for certain guys, he shook up the main event scene when they desperately needed something new in 2002, and it's very possible that he could have become a truly big draw on his own terms if he had stuck around, but despite WWE overpushing him so hard in those two years, and literally called The Next Big Thing, he really didn't leave that much of an indentation on WWE's business.