Switching REU recommender, good excuse? My professor who I thought would write me a stellar recommendation recently ceded that he feels he must be up front in my recommendation letter and say that I am disorganized.

I have confronted him and asked him to overlook my pitfalls, which he cited as: disorganized, asked for web assign extension, and failure to follow his strategies.

I received a 100% on the final and an A in his class and he also told me during the semester I was his favorite student in my class.

I applied to twenty+ programs and can still alter a lot of my recommenders listed. Of those that I cannot, what excuse should I do to switch recommenders?

I have three other professors who are willing to write the recommendation.
Your recommendation letters should help you in any admissions program. They should speak to your strengths, but also be honest. If you feel that this professor will write something that can damage your application and you have the ability to switch out references/recommendations in your application without negatively impact your application, then absolutely, you should have another professor write you a recommendation letter. For the ones where you cannot switch, you should be honest in that you have another professor in mind who can write you a much stronger letter of recommendation - which is not a lie.