Time to enter psychologist mode here...
We've all heard cases on the news about people getting kidnapped. A lot of them have problems and almost appear to take a step or two back from the point they reached when they had developed. If you got kidnapped as often as Peach, I'm sure you'd exhibit signs of not appearing too bright sometimes because of the trauma it caused.
To further back up this point--sometimes, there are conditions that are the result of kidnapping (Stockholm Syndrome comes to mind in particular but I'm sure other conditions could develop--this would be an interesting study to conduct).
Let's add to this another variable--Peach's age. I'm going to assume she is 23 in the first game and because video games can distort things, this age remains constant over time (in other words, she is 23 in both 1985 and 2009 as well as every year in between). Folks going through this time in their lives are still developing in many ways. Mental capacity, physical strength, and brain development have yet to peak. It's also at the beginning of Erik Erikson's "Intimacy vs. Isolation" stage, and Peach may be regressing because she doesn't have a steady love partner in her life (Mario does not count since she is kidnapped and isolated from him a good bit of the time and also because I can't see them spending every waking minute of their lives together--after all Mario has to unclog toilets and fix shower heads). Failure to "pass" this stage in life may have led to a good deal of depression, which can cause mental performance to lag due to feeling down. Mental performance and capacity can also appear to be limited when trauma is part of one's life--ask a former POW about this one.
From my observations, Peach is probably a very intelligent young lady, but various psychological factors don't let her true mind shine through all the time. However, her personality appears to be unchanged by any of this, which is evident when she throws mushrooms to Mario in SMW even when she's being held hostage inside the clown copter.