I am coming back from the dead (haven't posted here in ages) to share my thoughts on this subject, since I am very interested in it.
First of all, I agree about the fact that pretty much all girls in the show are more "science nerds" than "geeks", meaning: extremelly intelligent, amazing at science, interested in scientific subjects even in their spare time, but not interested in comics, mangas, sci-fi movies, novels, tv series, table top games, videogames, etc... And I mean "science nerds" as a positive quality. I know that the term "nerd" usually has negative connotations, but that word is definitely a compliment in my dictionary.
Secondly, I think that most girls and women here really like Leslie, Bernadette and Amy. I certainly do! Amy was a flat and boring character at first (as someone said, a "Sheldon 2.0"), but she developed in a very interesting and funny character towards the end of the season.
In my opinion, there have been a lot of episodes in S4 in which the on screen time with the girls was as fun as the on screen time with the guys. This is definitely a big improvement!
Actually, this is pretty much the only thing that I like of this season, as I find the rest too mainstream, with the geeky elements and science "dumbed down" for the wider audience.
What's missing, IMHO, is a female character that shares the same love for comics, sci-fi stuff and games that the guys have, with the exception maybe of Leslie and Penny, though their interest in these things is only marginal.
Ages ago, I complained that, as a female who is a geek, I didn't really feel represented by any female character of the show. This is still true, though things got a little better with Amy and Bernadette.
There's no female character I can really identify with... but there's still hope for the next seasons!
I think that having strong, smart and fun female characters that don't rely on their looks and place other things above being rich and beautiful is already a big improvement compared to what we usually see on TV or in the movies.
Forgive me for the long silence and for the long post that doesn't really add anything new to the discussion... Also, please do remember that "science nerd" is something I consider a positive quality.