Christopher Lee said:
^Where I draw the distinction between the two instances is that Yoda was shown instructing multiple students (and served as a surrogate mentor for Obi-Wan following Qui-Gon's death), whereas Dooku's master was created specifically for the novels and had no basis in canon.
Obi-Wan not being Yoda's padawan would fall under "what do you hate about the prequels", and the prequels' problems don't make the EU's any better.