I found a quote from someone on AVClub that explains Bernadette and Amy's characters:
"Bernadette's was retconned in season 4, by a line where Bernadette says she played naive (for the most part) to Howard to protect his manhood because she's smarter than him. After this is mentioned in her next appearance Howard is threatened by Bernadette's tall ex. Which I presume is when she stopped playing as naive, after their relationship survived that. Later on, she starts showing him her mean streak, that gave us Bernadette as we know her today.
It's a flimsy retcon I'll admit, but I can let it slide for the most part, because up until that episode revelation, Bernadette didn't share screen time with mostly anyone except Howard.
Most of her outlook was for the most part manufactured sabotage of herself that came from her giving up on having friends (or anything beyond that). At least when we first met her.
Once she became BESTIES with Penny (who she perceives as a popular girl) you can see her trying to be clingy and sometimes pushing the boundaries on what she should be doing as a friend towards her. Once her friendship kept growing, she kept opening up, and opened up her mind to more possibilities. The "robotic monotone" in her voice stayed until about the third episode in season 5, then she started talking more normally and expressing more emotions, instead of keeping her emotions bottled up. I think they handled her transition alot better from who she was then to who she is now.
Now was that the plan for her to be like that in the long run when she first started making more appearances in season 4? I doubt it, but sometimes you figure out different things about the character(s) when you write them or have them say other things or interact with different characters."