I sided with the with the Alik'r for a few reasons
Saadia's story had a lot of inconsistencies and I mean a lot. She says that she spoke out against the Thalmor in Hammerfell and they hired assassins to hunt her down. This doesn't make sense, everyone in Hammerfell hates the Thalmor. They had a war with them and no Redguard would ever support the Thalmor lest work for them. The Thalmor have no influence in Hammerfell as the Redguards pushed them out during the war. It wouldn't matter if she spoke out against the Thalmor because literally everyone in Hammerfell hates them already. Also knowing the Thalmor, she would have been dead already if she was really being hunted by them.
Kematu's story makes way more sense than Saadia's. His side of the story is that she sold out a city of Hammerfell (I can't remember which one) and because of that it fell during the war causing hundreds if not thousands to lose there lives. If you side with the Alik'r, later on there is a possibility that you will be attacked by Thalmor Justiciars with and execution order. Why is that? It is probably because you helped the Alik'r find someone they were protecting. I just have a gut feeling that Kematu is telling the truth, his story seems to make a lot more sense than Saadia's. Most Redguards that you meet in the game seem to be honorable people and I feel that Kematu is no different. They have no reason to help the Thalmor, all Redguards hate the Thalmor with a passion because of the war.
Just a side note: If you read the article about the Great War and get to the section telling about how the Thalmor were pushed back across the Alik'r desert it states that they were harrassed by Alik'r warriors the whole way. I doubt the Thalmor would go looking to them for help rather than just doing it themselves.
I'd like to know which side you guys picked and why. Also if you have evidence of one side being right and the other being wrong post that too!