1 - She hasn't been actively using/depleting her Divine powers to the extent that Vivec has.
In certain texts it mentions that Vivec is by far the most widely traveled of the Tribunal and is their public face. It's possible that between all that and constantly shifting into alternate dimensions, he eats up quite a bit of his Divinity on a regular basis.
Almalexia on the other hand is secluded in her fortress and doesn't even heal or walk among the people any more. I think because she's greedy to hold onto her dwindling powers.
2 - She was a higher class in society than Vivec. This is not confirmed 100% but in certain lore she was spoken of as a Queen of Morrowind even before she was a god. She was the wife of Nerevar whereas Vivec was a simple advisor and son of a Netchiman. Perhaps "highborne" Dunmer have slightly stronger souls naturally.
3 - Her "character class", in the RPG sense, was more physically imposing than Vivec's. Whereas Vivec combined elements of the Thief, the swordsman and the rogue, Almalexia was a flat out holy warrior type, the closest thing to the classic DnD Paladin which exists in Dunmer culture. It's possible her lifestyle and training conditioned her body and spirit to be much more durable than Vivec's. Even though Vivec was a mighty expert swordsman trained by some of the best, his true abilities were of word craft and subtlety. Therefore logically he'd have a lower vitality than her.