I always find this kind of thing fascinating, because I'm VERY good at recognising people and faces (and pretty good at drawing them, which seems to be connected), it's one of my very few innate, untrained talents, and to me, they're not even that similar. Like, Eisenberg has quite a strong, masc face with a more distinct and pointy jaw and much heavier features than Cera, who is sort of the archetypal wimp. It's almost like Chad Eisenberg vs Virgin Cera. Eisenberg is also usually significantly heavier built, has a shorter neck, has curly hair rather than messy straight hair, and blue eyes rather than brown. I'd say he's considerably more conventionally masc-handsome too.
He's also a more talented actor than Cera, and cast in pretty different roles. Like I can't think of a single Eisenberg role you could just have cast Cera in to roughly the same effect, nor vice-versa. Like, if you put Cera in The Social Network it would have had a totally different tone, because he just doesn't do intensity in the same way. Most Eisenberg roles if you cast Cera it would just seem sarcastic, and if you did the reverse, it would seem weird, like Eisenberg in Scott Pilgrim would just not have worked.
I think what this proves is that like, about 60% of people (source: arsepull) are kinda face-blind, and identify people only by like very broad categories of facial features like "big nose" and "wide face", and by height and their hair-shape (I have a friend who is fully face-blind and he absolutely uses hair-shape a lot), because that's the only way I see this working (neither is tall - Eisenberg 5'7" and Cera 5'9").