Correct on all points, except one -- it's not really "borderline" incestuous. I mean, the main character says how he's holding off on going after his sister until she's of age, which is a pretty clear statement of incestuous feelings and intent as far as I'm concerned, and of course it's moronically idiotic, but almost everything about the series is.
The only worth there is how over-the-top it is sometimes, and the lengths the author goes to to show how much smarter the MC is than every other thing ever alive.
Nah, that's just the author's way of showing how totally not overpowered his insanely overpowered protagonist is. I mean, the setup, as you say, makes it seem like he's "weak", that humans are weak, etc, but it's a blatantly obvious setup for his insanely overpowered invincible brain to save the day and defeat all foes. It's just a slightly differently-worded version of the same usual stupidly-overpowered-protagonist issue you frequently see in (badly written) shonen, nothing more.
As for the little sister, she mostly seems to just go along with his ideas as far as I've seen, though I admit I only watched a few episodes. She's supposedly "as smart as he is", but of course it seems to always be him with the ideas, etc. Her main function is for disturbing loli and loli-incest fanservice, most of the time... and, like the usual 'sidekick girl' character (as with Trinity Seven's MC's magical book) going along with just about any fanservicey idea the author wants to subject the female characters to. I mean, yeah, she's smart, but there sure seems to be a MASSIVE imbalance in which one of them actually does stuff, in the male lead's favor of course.
