Clearly Mr. Collins is self-obsessed, arbitrary, dismissive, and lacking in both education and common sense. But as to his ability to father intelligent children, I wonder. Could much of Mr. Collins's manner be due to how he was raised, by a miserly and ignorant father? Were Collins an only child subject to the whims of an uneducated, selfish man subject to bitterness over wrongs against him, actual or perceived, he could well have intellectual gifts left twisted or undeveloped. So his genetic promise might be greater than we would imagine. Certainly people of Charlotte's era would never know. Let us just hope that Charlotte can maneuver both Collins and any eventual children to give them a better upbringing than their father suffered.

Will Charlotte have regrets during her marriage? The question to me is not whether she will have them but how often and long-lasting they will be. I expect most people have some regrets during their married life; but Charlotte may at such times reflect whether she would be happier alone in the world or dependent on family and decide she is not as bad off as she might be. (I guess I assume her husband is not abusive, but as you say, who could tell at his point?)

One point of your post prompts me to ask a question about entails. If Charlotte has a son before Mr. Bennet dies, does she not still have a chance of inheriting Longbourn on his behalf if no closer relation exists? IIRC we never hear of a Collins brother (other than in Lost in Austen, LOL). No doubt Lady Lucas has been inquiring into Mr. Collins's family tree almost as eagerly as she has been computing actuarial data on Mr. Bennet. So I think Charlotte might still survive her husband's pre-deceasing Mr. Bennet. I expect Charlotte would want to try for an heir as soon as she can regardless, if only to avoid Mrs. Bennet's worries.