I don't like how CBS has a single set of bids/drops that you can enter, and how they get automatically prioritized based on bid. Let's say I want to drop a guy and would like to add a cheap SP as my first priority, but if I miss out on him then I'd like to go for a guy that just took over the closer role as my second choice. There is no way I could do this with CBS without severely overbidding for the SP or underbidding for the closer. Just because a FA will cost more to acquire doesn't mean they are the highest priority or the best fit for my team for that given transaction period.
On the flip side, OnRoto has a system that allows the kind of flexibility I want and more. You enter multiple sets of claims, one set for each player you want to drop. These sets are prioritized by whom you most want to drop, and within each set you get to prioritize your bids regardless of the bid amount. Further, if your league uses a waivers system as well as FAAB (we do), you can also mix waiver claims amongst your FAAB bids and set the appropriate priority for who you most want.
I'm told with CBS the commissioner must manually set the salary after FAAB processing. But with OnRoto, RotoWire, and maybe others that gets set automatically to either the winning bid or some default value based on league settings.
I'll agree with you that CBS has almost everything nailed. Solid, intuitive UI that provides loads of info in consolidated views so you can use it with ease. OnRoto doesn't. But for some, the huge difference in FAAB contingency bidding is more important. I guess I'm greedy because I want a site that has the best of both.