I'm sorry for coming across as a dick, but the idea that you "wasted" time learning a framework that became obsolete is silly to me, and it seems to be a common sentiment.

Ask yourself: at the time you used prototype.js, did it save time on the project?

If you answered Yes, then it was never a waste of time. Knowing prototype.js AND jQuery makes you a better developer: you learned the hard way that abusing prototypes can lead to hard-to-understand code. That can only be a good thing!