I think the biggest negative of TSM and TFM is playback speed. The rigs are reliable and you know what you’re going to get, which is nice, but they can be really heavy (particularly TFM). I’ve heard of some people using TFM as an intermediate step – to quickly get face controls that enable them to sculpt blendshapes easier, and then they ditch the rig and just hook up the blendshapes themselves. Seems cool but I haven’t tried it myself.
TSM also has some weird choices from an animator’s point of view, such as when you switch to FK spine, you lose the independent hip control (both root and hip controls rotate the torso unless you’re in IK spine). It may seem like a small thing, but having the independent hip can come in so handy, which is why I really dig Rapid Rig at the moment (though I need to check out Advanced Skeleton! thanks djx).