Well, they're also just bigger - the bigger the boat, the more difficult it is to get under (at least if you keep in mind that all boats of the era were trimmed primarily for surface cruising)
The largest U-boats (IXDs) were 1800t submerged, while even the smallest fleet boats (P class) are 1960t submerged, and the Gatos are over 2400t. The Type VII is a puny 850t by comparison.
For their size, the fleet boats actually did really good. They improved their diving performance by a lot over the course of the war, and if you're playing TMO - look out for those crew skills that might help cut diving times. In many cases it really was the crews knowledge of the boats that allowed them to get under quickly. Don't expect anything much faster than 40 seconds though!
[edit] funny how Ducimius just said what I was thinking!