Oh My god this was bugging me so bad!
In Act1 Raph actually tells you he won't make a deal with you yet because you are too "Eager" and wants to you come begging crawling on your hands and knees when all hope is lost.
But then in Act 3 He comes to you while you are essentially holding ALL of the cards. You at this point know about Orpheus, You potentially know about Vlaakith, you know about the Emperor, you know about the Crown of Krasus. You know especially that while you are under the Emperor's protection you cannot succumb to the Tadpole, you know you have a clear goal and where you are need to be to accomplish said goal. Not only that, he gives you his Ace by telling you about the Orphic Hammer, and that he has it, in it house. Then he tries to make a "Deal" with you that only benefits him? Worst fucking Devil ever. As a DM this has bugged me so fucking much. If anything you should be able to make a deal with him LOOOOOONG before you learn about the Emperor, or how or why you are being protected. His Scheme makes zero sense, at no point does he have the upper hand. Thanks for telling me about the magical hammer jackass, I'm going right to your house and taking it now!
Or Hey, you know what would be great, if there was permanent consequences to using tadpoles and their powers that added up throughout the game. Raph could leverage that to make his deal with you. Maybe they erode your soul and cause permanent damage to you in some way, but Raph can replace that part of your soul with his deal.