My car hit 40K miles and needs the transmission service. I found out my tranny was making a noise and it needs a new tranny under warranty.

I have pre-paid maintenance which covers the tranny service, but since I'm getting a new tranny it won't need the tranny service.

Anyone have any advice on what I should ask for? Or just let it go since I'm getting a new tranny.

I basically paid for tranny service and won't be getting the service.

I think you hit on the right outcome, but may not be ready to accept it. Let it go. Don't think of paying for the actual fluid, etc. in the service. You paid so that at 40,000 miles, your trans was in the proper condition to keep going to the next 40,000 miles. That objective has been accomplished with a trans service unlike any other....replace the entire trans!! I'd say you got at least what you bargained for, and MBUSA didn't make a dime on you. They lost money, if somehow that balances out the justice of the situation for you. Only the dealer comes out a bit ahead as he gets to bill MBUSA warranty for the longer labor op of replacing the entire unit.

+1 on let it go. At the least, maybe they could owner your unclaimed service on your next fluid change at 80k