Its a comedy. It's going to go for the laugh. The "odd things" are where the humor is going to come from. Even sit coms built around wives, children, pets and hobbies will go for the laugh derived from those elements. And those elements will exaggerated to generate those laughs. Be it a Tim Taylor on "Home Improvement" or an Abed on "Community". BBT is no different. The characters are also shown to be highly intelligent and successful in their careers. They have relationships and one has gone from a sleazy guy who hits on women to a guy who's engaged to be married and thinking about having a family.
I think the fun house mirror analogy went over your head. Which I find odd for someone who's suppose to be a fan of Science Fiction & Fantasy.
And I think folks defending the show are missing the difference between someone laughing "with you" vs "at you".
When a show like Who or Trek makes a meta-joke, like Riker over-explaining how the ship works to that Ferengi in "Rascals", that's laughing "with you". The only times I've seen this show, they're laughing "at you".
What I don't get is why you identify so much with the characters on the show as to define them as analogous to "you" when jokes are made at their expense. Sit-com characters are always exaggerated caricatures designed to elicit humour. They're not laughing "at you"; they're laughing "at Sheldon" (or whoever happens to the butt of the joke at the time).
Taking the humour to heart as a personal slight seems like over-reading the intent of the gags, as well as giving too little credit to the ability of most people around you to separate reality from fiction. In any event, they not even that insulting; generally, they're pretty mild pokes with some nuance.
In terms of influencing any sort of national or global perception of what SF-fans are like, then again, this only matters if someone is as extreme, narrow and socially-inept as the characters in the show. Assuming you have a more balanced life, it isn't going to make the blindest bit of difference how someone views you or indeed affect you in any sort of way. So I can't say that I see the practical problem.
I don't write the above to in any way suggest that you don't have the right to have your opinion; of course you do. But I think it's a shame in terms of your missing out on a few good gags and funny situations.