From the Thalmor dossier on Ulfric:
"Status: Asset (uncooperative), Dormant, Emissary Level Approval
Description: Jarl of Windhelm, leader of Stormcloak rebellion, Imperial Legion veteran
Background: Ulfric first came to our attention during the First War Against the Empire, when he was taken as a prisoner of war during the campaign for the White-Gold Tower. Under interrogation, we learned of his potential value (son of the Jarl of Windhelm) and he was assigned as an asset to the interrogator, who is now First Emissary Elenwen. He was made to believe information obtained during his interrogation was crucial in the capture of the Imperial City (the city had in fact fallen before he had broken), and then allowed to escape. After the war, contact was established and he has proven his worth as an asset.The so-called Markarth Incident was particularly valuable from the point of view of our strategic goals in Skyrim, although it resulted in Ulfric becoming generally uncooperative to direct contact."
TL;DR - Ulfric was broken by the Thalmor under interrogation and his interrogator is now the Thalmor advisor to the High King (to Ulfric if the Stormcloaks win). In other words the Stormcloaks are, albeit unknowingly, dancing to the Thalmor's tune so siding with the Empire is the only real choice under those circumstances.
"Status: Asset (uncooperative), Dormant, Emissary Level Approval
Description: Jarl of Windhelm, leader of Stormcloak rebellion, Imperial Legion veteran
Background: Ulfric first came to our attention during the First War Against the Empire, when he was taken as a prisoner of war during the campaign for the White-Gold Tower. Under interrogation, we learned of his potential value (son of the Jarl of Windhelm) and he was assigned as an asset to the interrogator, who is now First Emissary Elenwen. He was made to believe information obtained during his interrogation was crucial in the capture of the Imperial City (the city had in fact fallen before he had broken), and then allowed to escape. After the war, contact was established and he has proven his worth as an asset.The so-called Markarth Incident was particularly valuable from the point of view of our strategic goals in Skyrim, although it resulted in Ulfric becoming generally uncooperative to direct contact."
TL;DR - Ulfric was broken by the Thalmor under interrogation and his interrogator is now the Thalmor advisor to the High King (to Ulfric if the Stormcloaks win). In other words the Stormcloaks are, albeit unknowingly, dancing to the Thalmor's tune so siding with the Empire is the only real choice under those circumstances.