The pro for a transmission drop is that it's cheap and easy.
The con is that you've lifted your Jeep so that it'll do better offroad, then you lower the bottom of your Jeep so that it scrapes across rocks.
As for motor mount lifts, you should do a bit of research before doing that. The overall idea is that you raise the front of the engine which straightens out the drive lines a bit. It may help with minor driveline vibrations. Motor mount lifts are normally used as part of a high clearance skid plate setup.
Both of these options are affordable ways to help with driveline vibrations. The right way (assuming you've got the cash) is to get a slip yoke eliminator. There are a few threads that may help
http://www.jeepz.com/forum/cj-yj-tj-jk/33989-removing-transfer-case-lowering-kit.html
Honestly, you shouldn't have to do any of this. Just pop the lift on and see if you have any vibrations. If so, install the lowering kit (which is most likely included in your kit), then take your time and decide if you want to change anything.