my friend, im so sorry but i have to contradict your first statement, madara had the ability to control the fox thru genjutsu / hypnotism...and that was because the fox was alone...how many times does the story need to tell us that genjutsu or hypnotism doesnt work if you have a partner to wake you up...? did you remember what 8 tails said about genjutsu? please re-read the manga...
and my answer to your question is:
1. first and foremost madara knows his secret, (maybe the weak body that nagato has) even he has the most powerful eye technique, the user is still weak which becomes very submissive to attacks...maybe even an explosive tag would pawn his true body...
just take note of this:
eye technique vs eye technique = nagato wins
physical abilities vs physical abilities = madara wins
just how do you think nagato will hit madara in his present condition? maybe he would maybe he wouldn't right? its because madara can move freely on his own body...unlike nagato strapped in a chair, eventho he uses strong jutsus the likeability of hitting him is big, because his immobile...or maybe has poor mobility...
yes you are strong but if you are not good at dodging even weak attacks you'll certainly fall...
2. summoning technique relies on the body who has a blood pact with the creatures, that time it was animal realm's body who summoned the creatures, logically speaking if you knock the summoner out, the creatures would disappear as well...play magic cards
overall i still agree with what you said especially the last one wherein naruto + sasuke vs madara or whoever the ultimate villain is...of course, its naruto's heroism in the end cuz he's the main character afterall...
:naruto: + :sasuke: vs :akatsuki: <---- by the way what happened with this leaf guy?