Humans sort of adopted an adjusted version of the elven pantheon after Alessia tried to make a sincretic religion between what humans worshiped up to then, and the Ayleid gods (not counting daedra worship). So that's sort of why that caught on, it was an attempt at cohabiting with the remaining Ayleids who held all the technology, architecture, and military power (before the Imperials decided to kill off all the innocent Ayleids anyway).

Regarding the elves, the Altmer weren't the Ayleids, so if Akatosh made a pact with Alessia the Altmer wouldn't particularly care, because they didn't lose anything. Bosmer as well. And the Dunmer never worshiped Akatosh.

Also, humans don't see Lorkhan as evil (except for the Redguards). Nords actually do worship Lorkhan, but they call him Shor, and the Bretons call him Sheor. Reguards call him Sep, and he's evil for them because of their whole philosophy regarding the Walkabout, but that's a pretty long discussion.

Incidentally, the Dunmer - though I'm not sure it's ever made explicit - are the only elves who don't see Lorkhan as evil, because of their own philosophy. Lorkhan took away immortality from elves, and stuck them in an uncomfortable mortal existence, but Dunmer believe that sort of adversity makes you stronger so they respect it.