I believe they're basically the same sub but the VTF-3 is tuned a tiny bit lower (22 Hz vs. 25 Hz) and has a switch that lets you plug one of the two ports and tune a bit lower still (18 Hz) with less output but slightly better deep bass.
If you were likely to leave the VTF-3 in "maximum output" mode (22 Hz) then the difference is tiny. At worst, you're going to get a bit more output overall at the expense of a bit less of the deepest bass.
If your question was "STF3 vs. VTF2 Mk 3" then I think it depends on how loudly you want to play. If you have a heavy hand on the volume control then you will be happier with the STF3. If you don't play very loud but want the most deep bass then you might have been slightly happier with the VTF2 Mk 3.
If your question was "STF3 vs. VTF2 Mk 2" then you definitely made the right choice.
EDIT -- I *hate* answering questions like this after the purchase decision has already been made
