The problem with the saveas is especially apparent if you try to send someone an exported assembly. When they try to save, they will run into the duplicate filename problem, there is no other option besides renaming the parts with unique names.
But how does putting the duplicate parts into separate folders help? You still have to have unique part names, whether in a separate folder or not. Why would you want folders named #10-32-1, #10-32-2, etc? I do have separate folders for hardware, and one for common parts between different assemblies, but would not want one for duplicate parts in a single assembly. It all depends on the nature of assemblies you are designing. I have about a dozen assemblies I'm working on right now. Among the 12, 1,2, and 3 share a few parts, but most are unique. 4 and 5 share a few, etc. But they all use common hardware, and there are a few parts that they all use. I used to just export a step file to work on at home, but the saveas problem makes that impossible. Now I just export my 1.2gb repository to take back and forth. It just wastes a lot more time creating and importing the snapshots.
Also, if you have a single non-hardware part that is used multiple times, having to put them in a separate folder besides the one where the rest of the parts reside wouldn't help me much either.
The bottom line is that they need to fix the saveas behavior so it works just like save, without any problems with duplicate parts.