Especially when a document is opened in a way where you don't yet know if/where it's permanently saved (as from the web), it's now much harder to find out where it is and make sure you have a copy where you want it.
I think this behaviour change is very good, it just doesn't fit our expected and established workflow. People just can't get around not having a 'Save as', when duplicate is probably closer to what they actually want to do.
If I have a Keynote file open, and I want to split off a new file so I maintain my old file, File->Duplicate and I'm done. I don't have to tell the system where to save it yet or anything. Once I've made my change, File->Save and it gets saved to a specific location. All the while, my original is there to reference and is intact. If I'm not ready to save it, I don't have it. It automatically is saved as long as it's open — even if I close Keynote.
A 'Save as' workflow would mean I'd have to File->Save as, name the new file on disk, make my changes then save again. If I wanted to reference the original file, I'd have to go back to the filesystem to open it again, or use a recent menu. This way has more context changes and app switching.
I'm not saying the old way is bad, just that the new way is probably better given the iCloud enhancements coming in 10.8. People have been forever using 'Save as' workflow to keep a template of a file, then save off their edited copy. Maybe this just isn't a great way to do it in the first place.