My understanding is that they want to end it on their terms, and they don't want someone else to beat them to it.

I have three Altmer, soon to make the fourth, and I see no problem with them. Hating the Altmer because some of them are impolite is just pure rubbish. I dare say 4 out of 5 Altmer are normal or polite (Calcelmo, Niranye, Faralda, Fasendil...) I actually know only two non-Thalmor Altmer that are selfish morons and that's the two shopkeepers in Solitude. Otherwise Altmer are very decent folk.
And as a poster above said judging all Altmer because of Thalmor is wrong in so many levels.

Despite what load screens tell us Altmer are generally accepted in Skyrim, unlike Khajiit and Dunmer for example. Virtually every named Altmer in this game are in respected positions such as shopkeepers, researchers and Jarls' courts.

Ondolmer is also a very likeable fella. And he is a Thalmor. Well, he always seems to be nice to my character anyway.

Nah, I don't like him. He's one of those dead set on proving his superiority. Some of these Thalmor and Nords are all the same.

Anyways, what I heard now is that Altmer even do more melee damage, because of the height. An 8% bonus apparently. Despite what I said above, they might actually be superior. They're already great for mages as it is.

i read somewhere in a weathered tome that younger altmer are looking for change and rebelling, some through terrorism. make your guy young.

One of the Imperial Legates mentions witnessing a Thalmor attack on Altmer refugees in Hammerfall. Have your character be a survivor whose family were killed in the attack. That or make them an Altmer from Cyrodil who fought for the Imperials in The Great War. Lots of reasons why an Altmer might oppose the Thalmor.