The Empire had to surrender to the Thalmor because for the good of the people.
One could argue that it was so the emperor could keep his crown, and if not, still a stupid decision.
As we all know that the Thalmor likes to kill people that do not think as they do and if I where the Emperor I would have done the same thing.
Yeah, and the Thalmor are doing just that. The empire gives them free reign to do just about anything they want. The empire betrayed the old and loyal blades, my favorite faction since I saw them in Oblivion, and for that alone, for destroying possibly their greatest chances of beating back the Thalmor I will never support them.
So my updated pros and cons of both factions:
Stormcloaks:
Pros; They fight against the Thalmor
Cons; they are a little racey, but nothing (at least not indiscriminately) genocidal. This is subject to change through the dragonborn's counsel. Compared to the Thalmor's indiscriminate murder torture and oppression of anyone is isn't elven, and who worships Talos, this is nothing.
Empire:
Pros; basically nothing
Cons; They betrayed the blades, their own people, and the blades (arguably their greatest asset). The Thalmor control all of the empire with the emperor a mere puppet. Also consider that the empire has no plans to conquest against the Aldmeri.
Summary: Aside from a few npcs that reside on the imperial side that are actually good at heart despite choosing the wrong side, the empire is indeed long dead. The bittersweet ending of the stormcloak civil war quest was enough to get me to try out the empire's side, but ultimately the truth is that much more obvious and I see it even more clearly.
Anything truly good that remained with the empire died with the Blades. The empire basically ordered their execution. In the end the stormcloaks are the only logical choice. Skyrim is not weaker without the empire, but stronger. If the empire truly does have any fight left in them, any hidden desire to drive out the thalmor, they will side with Skyrim against the Thalmor after Ulfric is made high king.
Also I updated my OP.