VPT is amazing, I don't want to give the wrong impression, but there are a few key issues that prevent it from being fully usable in my opinion.
1) Autoplacement of cards. This is a pretty important one as it allows play to be significantly faster.
2) The messages when viewing players graveyards are not needed as the graveyard is public information during a game. Furthermore, it seems that you cannot view a players graveyard if they are looking at it.
2a) Regarding message spam, there is no need for a message when players move cards on the battlefield or hand. At the very least, suppress the message if it would repeat itself, ala MWS.
3) The ability to sort a zone of cards when searching it, like you can in MWS. This is needed so you can quickly find lands for example when cracking a fetchland.
4) Currently, the mtg module rolls a die automatically then draws 7 cards. This is incorrect, since players must first determine who is going first (the dice roll), then declare if they are going to play or draw. A minor thing but important for leagues and other tournaments which need to follow the rules strictly.
5) It is currently not possible to exile cards face down. The workaround is to put them onto the battlefield.
6) Dragging Auras, Equipments and Fortifications onto other cards does not attach them like they do in MWS. :3
7) The ability to quickly alter power and toughness witth Control/Alt +/- like in MWS. I apologize for putting so many "make it like MWS" requests but it did a lot right and the shortcuts are popular and help the games go a lot faster!
8) Not strictly necessary, but a legacy option to allow alt clicking for playing and tapping of cards would help people migrate from MWS.
On a more positive note, I am glad that VPT supports the new MTG Sideboarding rules. :)