My own thoughts on the subject are as follows.
If you routinely make well-fitted mortise and tenon joints, then a water-based blue (e.g. PVA) will cause the wood fibers to swell up and ensures a solid tight-fitting glue joint with minimum gaps and maximum strength.
On the other hand, if you make loose ill-fitting mortise and tenon joints, then you are going to need a glue with excellent gap filling properties. Even so, such joints are never going to be as strong or true was a well-fitted mortise and tenon joint.
The only good argument in favor of epoxy is its availability with long open times for complex joinery. However, there are extended open-time PVA glues (not as extended as Epoxy, but 2-3 times longer than regular PVA) for such applications. Unlike water-based glues, wood fibers do not swell when Epoxy or Polyurethane glues are applied, so water-based glues are usually preferred for such joinery since the swelling brings the wood surfaces into tight contact with one another.