malware can steals passwords saved, which are optionally saved encrypted. the cert at least in the one browser i checked is always encrypted.
and even then, if you have malware in your box, any and all security measures are worthless at this point.
decent Renegotiation and mobile client support will come if people using that on the desktop request the feature. it's like that for everything for a while now.
Managing the devices and revokation is also trivial. most sites does that very easily with API keys and cookies (e.g. google 2step auth, you can control which cookies are still valids for the 'remember this device' feature). the same logic could be used for client certs.