] I can't help but wonder what he must think, from time to time, about the differences between the two women,

I don't want to spoil future chapters :), but I can think of textual support that may infer that Charles also compares Anne to Mary from time to time. Though, I don't think such thoughts are in a manner that make him seriously wish he married Anne instead. (Or consider that it was such bad luck he ended up with Mary, for that matter.)

In fact, I don't think that all the love between Charles and Mary has flown out the window, as you say. I think Charles *is* happily married. He's not always perfectly happy, to be sure, but, as the narrator says, upon the whole and despite frequent little disagreements, he and Mary pass as a happy couple.

Off the top of my head, I believe that it is Charles's personality that is mostly responsible to their happiness as husband and wife. Aside from what is said by the narrator (that he has very good spirits that never seem to be affected by Mary's lowness, and that he bears with Mary to Anne's admiration) I think it's also his SIMPLICITY that makes and will continue to make them tolerably happy.

He 's a simple guy--he thinks simply, wants simply, finds enjoyment in simple things. He is not a highly intelligent Mr. Bennet who will eventually find disgust in and lose respect for his inferior wife.

Moreover, I think that the thing about Charles is that, though he might have been improved by a better wife, he, personally, wouldn't know--let alone appreciate--the difference.
My theory (figured out three seconds ago ;) is that: marry him to Anne or to Mary, and he would've been as equally happy either way. Sure, he would've been a better man with Anne, but I think his level of happiness (that easygoing kind usual with his type) would still have been the same as it is now with Mary.