I don't think I really have a favorite as well.
I play both. I have multiple careers in the different flotilas so I play a combination of VII's and IX's,and even a II in the Black Sea where you have to make every shot count with only 5 eels.
Both have their advantages and disadvantages. The IX's with their load out and long range make for some long patrols, but the VII's are pretty manuverable and dive quickly.
I just started back into SH3 with a VII in the Med after some time playing SH4. I sure miss having 24 torpedoes available in a Fleet Boat (and a ice cream maker too

).