It really is interesting how people can see things so differently. There's a certain clip I'm thinking off, from The Social Network, that is very Lex and subtly threatening, but I reckon you probably already know which one that is given that you've seen that movie. To me, he had presence there, albeit in an odd sort of way. I guess that type of villain appeals to me because it's realistic (I know, I know. That's a dirty word anywhere south of 2008).
We've had our share of James Bond type villains with their crackpot schemes and lots of "take over the world/universe!" warlords, but none of those seem like threatening, and more importantly, entertaining villains anymore. If they play into some of Eisenberg's strengths (and frankly, typecasting), they might be able to make something special. I'm pretty sure that I'd enjoy a fusion of a new age Zuckerberg/Jobs-type "nerd with power" with some classic Azzarello Man of Steel hatred and philosophies.
I understand your concerns and I'm not trying to talk you out of them. I just think it's interesting to see why some people are optimistic and others are skeptical.