Very true about "relative paths". I used to have the file set under "V1_0", now they're under "Current", and I copy the whole directory structure to version folders, saving the milestones.
It would be much easier to be able to just rename a folder and have it still compile.
Also, we run multiple projects, each having its own workspace. We also have a "Lib" folder serving as a HDL reference (not compiled, just copied to other projects). We use "Beyond Compare" to ensure consistency where we've copied HDL/software between them. Note this involves updating both the copies of the library HDL, as well as instances of them.
The ability to add comments (revision history) to the SOPC PTF and Assignments files would be useful (at the top of the file). Likewise for BDF and waveform files, with them being stored in a textual format.