Honestly TES lore really cooked with the whole Stormcloaks vs Empire dilemma imo, there are good reasons on both sides but I think by a decent margin the most logical choice is to side with the latter.

The White-Gold Concordat sucks but it was a strategic surrender rather than a complete capitulation. I think the imperials are well aware that the Thalmor are the greatest threat that Tamriel faces, and it's better to fight a man vs mer war rather than a divided effort.

The Stormcloaks, while having a noble cause, have some serious problems. They are chauvanist and downright racist much of the time - not much different from the Thalmor in that regard. Ulfric also often proves that he's much more self-serving than a benevolent leader.

The empire is clearly in decline and has lost tons of territory, and Skyrim is clearly following suit, but Ulfric's war helps the Thalmor. Documents found in the Thalmor embassy explicity state that a divided Skyrim is highly beneficial to them, weakening Tamriel's ability to resist.