If you have the time, please do the vb2 version first.
If not, just fully concerntrate on one for vb3
The only problems I see with doing a vb3 one is :
- who knows when vb3 gold will be released
- how long it wll take to get used to the differences between vb2 and vb3 and therefore how long it will take you to complet
- how quickly people take up vb3

I would say people will play with vBulletin 3.0 before they upgrade, seeing as styles form 2.xx will no longer work.

Cary from the vBulletin team said his 2.x.x Style converted nice and easily to 3.x

Only replacements get imported. The templates are not compatible.

But a conversion is not the same as reapplying a theme. If your design was not very modified, I don't imagine it would be all that difficult to convert it over. (header/postbit, etc)