Here's my two cents worth.
I don't think scoring is the main issue here? I mean, adding even 50k to your score via a spinner is nothing compared with stringing a combo together, which could be worth more than a million points. As long as you make sure the spinner "bonus" is indeed a bonus, and is not affected by any multiplier, I think the system is fine. No need for spinner caps or whatnot - that's overkill
The main problem I see with the spinner is the way it accelerates at the same rate no matter what radius you are spinning at. At the moment, it doesn't physically make sense and doesn't feel intuitive. My "one pixel spinning radius" method should be extremely ineffective because it is so close to the center of the spinner. Imagine trying to open a door by pushing near the hinge - it's much harder because you are not generating much torque (or "moment" for the engineers in the house). It should be the same with the spinner, at least physically anyway.
I just cracked out my DS and had a play on EBA. It confirms what I thought I experienced while playing it - spinning near the center of the spinner is very ineffective. The further out you spin, the easier it is (because of the longer "moment arm"). I'm not sure if this is the same in Ouendan - someone can probably verify this for me.
Of course, having to spin out further means you have to move your cursor more, which makes it more tiring
I hope that wasn't too hard to read.
eyupz