Pros
The number one thing I think Jaggaer has is/was the people. The teams that have been there or were previously created were great. I haven't been there in a little while so I don't know if it is the same, but I can honestly say that the people were the best thing about Jaggaer. If you are looking at Jaggaer right now, I can say that there is a great deal of opportunity to try and do new things where you get your hands wet in a great deal of areas. I am not sure it is the best long term option for growth, but you can definitely get some great experience stepping in the door.
Cons
Change happens, but how you handle the change is the biggest thing. Change can be good, bad, or go unknown. I think the change from SciQuest to Jaggaer was not the smoothest. There was a great deal of change and communication was not as open as it could have been. I know you cannot share everything, but there was a great deal of distrust from top to bottom.