My biggest issue with the points mod is the cheap customers it attracts. I can't tell you how many e-mails my clients get from customers saying "how come I didn't get points for this" or "I tried to use a discount coupon and I didn't get points" etc, etc. It is a great tool for increasing sales and encouraging repeat business, but it seems to bring out the cheap people en masse.
One other thing is that by default it doesn't display the current point allotment very well. Even on the BCS site when you go to check out you have to go back to see how many points you have first, and then do the math to see how many it takes to pay for your order. I usually put in a static page that explains how the whole point system works, and also display the point totals and calculations throughout the checkout process so people can clearly see how many points they have, how many their order will require, etc.