I wouldn't call it a waste of time considering the work required to level a gun is going to be done anyway. It just takes time and you have to be willing to swap the unleveled gun around characters and apply xp towards it while using the fully leveled version when you need it. Now that I don't have to swap many weapons, I go to the tower twice a day. Once to pick up bounties and twice to turn them in. No more time wasted swapping stuff around in the vault.

I tried doing it the "every guardian gets their own gun", but like you I had to stop as I kept getting more and more exotics and had to go back to tower on pretty much every mission to switch them out. Cheers