They mean two slightly different things. 'hear you well' means more that the sound is quiet 'hear you clearly' means more that the sound is muffled or distorted.

I mostly agree with Gary but I think they're essentially synonymous in every day use. I use both. I probably use 'well' slightly more just because it's shorter.

in daily use not much difference, but when you would say either is a bit like this. "I can't hear you clearly" is more likely to be used when communicating over a distorted radio. "I can't hear you well" is used when you did not hear because the voice was soft from the other person. A person with hearing difficulties might say either sentence. To describe either their lack of hearing, or the distorted sound they hear within their ear(s)

They mean the exact same thing. Saying I can't hear you very well is more common.