Stormcloaks win
-pro-The empire will lose a big province with much resources, divide and conquer.
-pro-seeing how "short sighted" Ulfric is, he will never make an alliance with the empire. even an alliance with Hammerfell will be filled with tensions, a problem which would never be present in a united empire.
-con-As you said, the Thalmor wouldn't be able to walk around Skyrim and take Talos worshippers and keep an eye around.
Imperial win
-pro- They still could regulate and stay around in Skyrim, spying and killing resistance to the Thalmor.
-con- an united empire is going to be hard to beat in the future, and there are no relation problems in this case.(which would be present if Stormcloaks win.
-con- Extra recources, means that the Empire can rearm its forces faster, much faster than the Thalmor can.
Please indicate how Ulfric is "short-sighted."
A united Empire also makes spying and intelligence-gathering easier, especially since they've already been doing it for a quarter-century.