I liked different things about the Yahoo and the FPL sites.
The FPL site was a better interface, and I liked that it did automatic subs for you if one of your starters didn't end up playing.
I liked the points system on Yahoo better. It seemed like players could get points for all sorts of things (e.g. passed intercepted, free kicks won, tackles won, etc.), whereas FPL was more just goals, assists, 90 minutes played, and shutouts (for defenders and keepers).
I'm kind of torn on the transfer rules. Since Yahoo allowed unlimited transfers each week, it made the sub players pretty pointless, but it also allowed you to really re-tool your team each week to better take advantage of certain match-ups.