Rinus Michels was the best manager ever as far as tactical awareness and innovations are concerned. His trophy count doesnt have the same zing to it as some other managers, but he is deffo the Godfather of modern footie.
While I agree with your Fergie comments, he is still my greatest, despite his tactical weaknesses, because he chooses amazing and tactically/technically talented Assistants while keeping everything else under his thumb. He is a pure winner and all he needs is the right type of support (like all the best top-tier management, you are only as good as your team - and he has drafted in some amazing people to complement his natural abilities).
Mourinho is different because he is a dictator, but he is tactically more astute, so he doesn't really need someone to complement him in that direction. Though he also has that knack of choing the right people for the job. He could have gotten rid of Clarkie at Chelsea, but instead he chose to keep him and they had a brilliant 2,5 years together (and it shows, what with Clarke leaving and Chelsea practically falling apart).
Also, I really do feel that you do Sir Matt a great injustice, because he created 3 super generations at United in the (50's/60's - forget which era) and made them great champions despite the Munich disaster. Something which completely destroyed one of the greatest football teams ever (Torino) was merely a blip on United road to success.
Also, he was responsible for Manchesters still famed scouting/youth system. He would recruit all the best schoolboy players and bring them through the ranks in the Bubsy way - which was not common during that time.
There are others, but the names elude me currently. More later, quite busy now...
Now i know Shankly wasnt as succesfull as other managers but the man was ahead of his time in his thinking of the game ,