In general terms, is it better to create an assembly out of individual parts or should one strive to use sub-assemblies?
Of course, if you are building a very complex design the sub-assembly approach might be the only way out. A car transmission, for example. This question might be more applicable where you do have choices. Small projects with a few dozen parts where you could consider going either way.
In the case of using the parts-only approach you'd endup with a directory full of parts and one assembly file.
In the case of using sub-assemblies you'd have the same number of part files. A few assembly files that are sub-assemblies and then your final assembly file.
I can see that a real mess could be had if you are not careful about in-context mates and how assemblies might drive the final model. It could very well turn into a real mess. I would also add that such an approach would no-doubt necesitate a project description file to let the next person know what the intent was.
The parts-only approach might be cleaner, but the abstraction level of logical sub-assemblies is lost.
Not sure...
-Martin