Great question!

Two points:
1. Each of us has a learning curve with each program. In my experience the worst are the car rental companies. I used to get my miles about 50% of the time. Now I repeatedly ask if my FF number is in the system and my miles come closer to 80% before I have to call or write. Needless to say, some of the "problems" are in the fine print.
2. I think an "average" can be ascertained by looking at Flyertalkers habits during the AA 20/20 promotion last summer. People seemed to feel that they needed about 5 "spare" partners to be safe. My family-of-4's experience was 97 partners, of which 9 didn't post without further communication (some quite extensive), and 2 never posted.

I don't see much overall difference from one program to another (United/AA/Hilton/...) but some partners are definitely worse than others, like Budget rent-a-car, and Best Western Hotels. It is mostly affected (I think) by franchise owners who have a vested interest in not understanding and not following their own rules.