I've heard that the Cisco Call Manager lacks many traditional features such as multiple call handling (ability to put a caller on hold and take other calls). Does anyone have a feature comparison list of any kind?

No you can put callers on hold and answer other calls. While they carry most features the only one they lack which I wish they had is paging through the phones. You can do this but it is purchase of software and server which is a rip off.
I think Cisco does need to work on their features though as they are just as not plentiful and easy to use as traditional pbx's.
From a technical point of view they could also make some changes in their system administration. Little things that phone techs like to have that are not their or it is a pain in the butt to do.