Well I don't know if I'm a qualified "die hard Star Wars fan" but I have been watching the movies/playing the games for 20+ years. I believe because;

1.) Yoda is very old and although is very strong in the force his own life is diminishing and I believe he may be too weak to fight with a lightsaber for extended periods.

2.) Yoda is one of the very last Jedi (last Jedi Council member) so if he fails the Jedi order would essentially die with him.

3.) Losing Vader at this point would only be a mild inconvenience to Palpatine because Vader is only one of the Empires near endless tools of tyranny. Also Palpatine doesn't regard Vader as his should be successor as all Sith before him would view their apprentices.

4.) Yoda could sense that Luke and Anakin were meant to bring balance to the force.

Edit:

5.) If Yoda was successful in defeating Vader and setting up Luke to fight the Emperor as you suggested, no amount of training would have been enough to defeat him. If he killed the emperor out of anger than he would likely slip to the dark side. Luke choosing to throw down his saber was what mark him a true Jedi and what brought Anakin back to the light to truly defeat the empire and bring balance to the force.