Personally, I would prefer it, because if it's a prequel, the creators had significant limits, they couldn't make major changes, develop some stories and characters, not disturb the world of TBBT.
I think Paige and Sheldon would have ended up together if it wasn't the prequel....because it seemed like it was headed that way. Plus, it feels like the creators have created an ideal partner for Sheldon. She's smart/genius like Sheldon (probably smarter) but with the personality of Penny or Missy (kinda), just more complex, messy, wit and later also sadder. They had complex relationship but they had great chemistry. And no offense to Amy, but Paige beats her in every way. Sheldon and Paige were close in similarities, they could complement each other in differences. Encourage each other and make each other better.
Maybe it's just me, but especially in the last seasons of YS, I was really shipping them and hoping for a romantic relationship between them... even though it was clear to me that it wasn't going to happen (just because it's a prequel and that we know from TBBT that Sheldon not only never dated anyone, but never even kissed a girl, etc.).