You have to stop thinking of Naruto (manga in general) as a real world and remember that it's a story. It's meant to progress and entertain us.
If Tobi used his Sharingan to control Minato then it would have been boring as shit to read. This is why he didn't do it. Plain and simple.
Why would it be? Do you realize that if that's the case then Uchihas can control naruto's world? Is Uchiha clan that great? It's plain and simple. Tobi can't use genjutsu on Minato. Think this way, if an Uchiha can use genjutsu that easily on Minato then there is no point reading this manga because they can cast genjutsu on shinobis below Minato's level and won the battle instantly. There are things Uchiha's can't do and there are shinobi's they could not defeat. I don't know who they are but one thing for sure Minato is one of those shinobi's. Every chap. in Naruto has a meaning that is why it entertains us to the max. This is the reason why so many debates arise.
Everybody in Naruto has a counter. For Uchiha, it's the Senjus. If Uchiha is that great as you claim to be then hashirama would be controlled by madara easily. What do you think is the reason why Madara loses the battle? Why didn't he cast genjutsu the moment they started to fight? I bet everybody would say that he didn't. For what reason? This also applies to Tobi.
Everyone is assuming Tobi didn't use genjutsu on Minato. Why would he not? Genjutsu is their primary weapon. Tobi knows about Minato and what he could do. Please don't tell me he doesn't know about Minato cause that's some stupid way of reasoning. Someone that has great knowledge about when the seals is at their weakest and for someone who knows where the jinchuriki will give birth means that he has a great intel.
Now, think back to the debate about Minato vs. Itachi. I bet everyone would say that Itachi will use genjutsu on Minato the moment they confront each other. That is their primary reason to win a debate. If everybody knows an Uchiha will cast a genjutsu against someone like Minato, why Tobi can't? Do you honestly believe that Itachi's sharingan is greater than Tobi when Tobi was able to control the fox?
Plot or not plot. We are entitled to our own opinions. No one is right or wrong. But, the moment the debate arises then there has to be somebody kicking someones ass.
Let us stop all the assumptions because it will go in circles. I can provide scenarios where Minato can defeat everybody and everyone of you can as well. If that's the case then the last option to seal a debate about Minato vs a Sharingan user would be.....Please prove that Minato is weak to genjutsu. If someone can provide that then well and good. Please don't provide examples where an Uchiha casts genjutsus on other shinobis because every shinobi has his/her own skillset. If this is the case then an Uchiha can cast genjutsu on the sage.
I am still confused and I really want to know the best answer there is as to why Tobi failed to cast genjutsu twice on Minato.
Thank you guys for sharing your opinions. I really appreciate it.