Jack -
I think you've summarized it pretty well. I've played in both types. My club's event is 54 holes...all "points"....formats are Chapman, Best Ball, and Combined. You can get away with some "ham and egg" play on the first two days, but there is nowhere to hide on the final day. I feel this format defienetely rewards those that played the best all week. But, the downside is you are only playing with 6 other people in those 54 holes, so not as social (we do some other things to make up for that I'd be happy to explain over IM or email).
The nine hole matches...obviously more social, incorporates match play (which is great), etc. The one thing I have never heard a good solution to is a good way to end up with the champions....seems like its a horse race (which is fun) but has to be handicapped and it all can come down to one shot or bad break (which I understand is golf), whereas the format we use better rewards those that have played well all week.
So in the end, it really comes down to what you are looking for.
Good luck,
Brad