Consuls do not get selected each year in Imperium, so your last suggestion would not work. Handling time from any given point; whether the founding of Rome or CE isn't really a difficult problem, given that its really only a matter of determing a "year 0". It's hard-coded at the moment, but it would be a simple thing to change. As a rule, though, familiarity is a good thing, which IMO makes it worthwhile to stick with the system that people can relate to (i.e., CE).
Regarding the deeper issue of your question, the problem is also related to the game framework. Obviously, something is not quite right with the design in a World War 2 game if World War 2 doesn't break out. Just as an American Civil War game would be quite strange without the secession.
Imperium, however, is not centered around the 2nd Punic War, so there would be nothing strange in a game without Hannibal marching over the Alps. Perhaps Rome lost the first Punic War. Or Carthage failed in its attempted expansion into Spain, thereby robbing Carthage of the base it requires to invade Italy. Or, simply, Rome and Carthage do not have no mutually conflicting interests at the time. Hannibal would still be there - he would just be occuppied elsewhere than marching up and down Italy. And after all, that is what alternate history was about. Rome and Carthage cooperated multiple times in history; a limited coexistence would not have been impossible. Of course, Rome's fear of external threats will eventually lead it to war with any power great enough to threaten it (at least that is the theory behind the AI design - paranoia), but the timing need not - and probably won't - be strictly historical.
