O.K. I'll take the bait (even though I'm not an expert and maybe I'm talking bs here).
9. If your country is low on "war important materials" it is much better to ride a lot of small type VIIs than just a handful of fleetboats. (We were always low on resources like steel)
10. The U-Boat can run with a smaller crew (so you don't have to write so many letters to the familys after your sub got sunk with you as the only survivor in front of your monitor

)
11. A U-Boat's silhouette is more difficult to spot because of the smaller conning tower and the smaller overall body.
12. The U-Boat can go deeper.
13. The "all hands forward" command will ensure that your crew stays physically fit.
So that's it for me (as I said I'm no expert and a lot of that stuff is based on what I've heard from someone who has heard that....).
What wonders me is that fleetboats were going three knots at silent running. Were they as quiet as the Germans running one knot? If not then I wouldn't call that an advantage.:hmm:
To Lukes 18th point.
U 2540 (NATO code Y 880) a type XXI served until 1968 and was later used as testsubmarine until 1982.

(Unfortunately these sites are in German but I bet you can find some English pages about that too)
http://www.janmaat.de/m_wbauer.htm
U 995 (type VIIc/41) was used by the Norwegian navy until 1962 (decommissioned in 1965)
http://de.wikipedia.org/wiki/U_995
And now the experts can tear me apart:p.