Deploying SSL partially is very dangerous, because then you have to be _very_ careful that the session ID is not compromised. I'd go as far as to say that it's virtually impossible to do that securely (for the average web site, built by more than one person who are not security experts, maintained under pressure over a period of years, and so on).
Someone else here mentioned SSL stripping, which is another problem, which you can't avoid [with partial SSL] no matter how much you try.
If you're deploying SSL today and you're not using HTTP Strict Transport Security, you're doing it incorrectly.
Encrypted tokens might help against CSRF, but if I have your session ID, it's game over. The best you can do is restrict the user agent used with the session, but that's an obstacle that can be overcome. You might try to restrict the IP address used with the session, too, but those change often even without attack that it's not practical, either.
The robustness of the public CA system is a legitimate problem, but it's not a concern for most of us. People like to complain that the public CA security model is not perfect, but we have to remember that the CA ecosystem was not designed for perfection; it was designed to enable ecommerce. We now have different goals (well, some of us) and have to change our approach accordingly.
MITM attacks using fraudulent certificates are very costly and make sense only against very high-value properties. If you're legitimately worried about them, you should consider using public key pinning, which effectively deals with the problem. (But, alas, only works in Chrome today.)
Performance issues (I'd say most are imagined, but there is definitely an increase in latency) and higher cost of deployment with SSL (essentially more expensive CDNs). Some sites that rely on 3rd party services might struggle to deploy full SSL if not all services support it.
In my experience, most people are recommending partial SSL because they're not aware of the security issues. For example, many developers "know" that you're supposed to use SSL only to protect login credentials.
Someone else here mentioned SSL stripping, which is another problem, which you can't avoid [with partial SSL] no matter how much you try.
If you're deploying SSL today and you're not using HTTP Strict Transport Security, you're doing it incorrectly.