Both have their moments, and Aeris and Cloud could have been a possibility if things had gone differently. However, even with the revelation that Zack and Cloud are different once the surface is scratched, there is a chance that Cloud and Aeris represent an "idea" rather than an actual love story. It is like with Aeris saying that she wants to meet Cloud (as in the real Cloud) if she is the one to date him during the Gold Saucer revisit - she wants to make sure that it is Cloud and not a reminder of Zack that she loves, perhaps? It could just as easily be that she is starting to fall for Cloud himself, from what little she does know about him (even Cloud doesn't even know who Cloud really is at this point), but I think there's a chance that she needed to be sure whether it was Cloud she was falling for, or if it was just Zack again.

Ultimately - I think Zack and Aeris, Cloud and Aeris, and Cloud and Tifa were all very much real at some point, even if they didn't last, had the remaining person move on, and even if Cloud did begin as a "replacement" for Zack subconsciously, if he did. In my mind, moving on does not render your previous relationships invalid - they will always be a part of you, even if they weren't the ones you were destined to spend your life with.