I like the IXB. Longer range, slightly faster surface speed, bigger deck gun (105mm), more ammunition, and more torpedoes. It's not great for dicey situations, as it doesn't dive very quickly, but as a submersible surface raider, it's a fine boat, especially in the early stages of the war.
One of my favorite WWII books is "Operation Drumbeat" by Michael Gannon. It follows the exploits of Reinhard Hardegen and his U-123, a Type IXB. It's an excellent read.