Both (the 999 and the 1999) seemed to be somewhat the same, only different was that the more expensive one had Sheet Metal modeling tools, more file formats support, team workflow tools and that "extra easy"(?, as the producers call it) surface modeling thing
Other than that both has the same base features (very similar to Inventor).
No year fees, unless you want to pay for the "Subscription Service" (extra support and all that)
Here is a link where you can see the differences in both versions (and download a 30 day trial):
Geomagic - Geomagic Design product comparison
*It seems that they have changed their product name
Please take note that this is just a recommendation based on my experience while testing different workflows for CAD apps, I'm sure both (Alibre and Inventor) will have some feature that the other won't