Before I even get started

When I read the first post in this thread I thought of OTE right away. Ron`s presentation of it is slightly misleading, one of the traits is supposed to be broad, the other two narrow.
To use the eyeball example, its main trait would be "Floating eyeball". This trait would be used for floating around, eyesight, freaking people out, and any other typical floating eyeball activity, whatever that might be. Its two side traits would be telepathic zap and cosmically wise, these traits have a much more narrow application, but serves to make the eyeball even more unique.
For a scifi game like this it would probably be a good idea to define race and homeplanet/culture/sector.

Fudge might also be used, but my experience with it is somewhat limited.

The system you outlined looks interesting, but apart from the problems you pointed out, it seems to me that it would promote standardization rather than diversity. Both a wise floating eyeball and a orc hacking barbarian would be portrayed using the same three pair of stats.
How would this system separate between a strong sword swinging barbarian from the Yrettab-cluster, a nimble four-armed pit fighter on the run from the law, and Jim Raynor, marshall of these parts?
If diversity is a goal in itself, then I think player defined traits is definately the way to go.