We haven't lost that something special any more than we lost something special when you compare corn to the original maize, or tomatoes to the original little red berries growing wild. You may have a mutt as a dog, but you don't have a wolf. Dogs were selected by us, humans. We've since overbred some.
Bees too have been being bred for thousands of years.
We've gained a lot of special. The original bees here were German bees...nasty black swarmy bees. Probably we'd have a fraction of beekeepers if we still only had those. But yeah, we probably lost some longevity there.
And it depends if you want to compare back to the original bee or just to the bees that we had a 100 years ago. If you are just asking if they are sometimes overbred and inbred? Yuppers, plenty of that going on too.
Then compare the bred bees to the ultimate natural bee: the africanized bees. Yeah...there's something special!! :-D
So we've had some duds, some mean bees, some weak bees, some swarmy, some runny...but overall I'd say they're pretty great!