Wow this is hard to choose, this is my view on both:
Kakashi:
This guy is the true definition of a ninja, one that endures. Kakashi has endured the most out of any other character, yet he still stands strong and keeps moving forward. What makes him even more amazing is that he probably has the most reason to have turned to the dark side, but no he still posses the will of fire. He has incredible mental strength, wisdom and intelligence, when it comes to analysing and formulating a plan, he is one of the best. His ability to stay rational even in tough situations and his cool demeanour is what makes him one of my favourite characters. He is probably the best all rounded ninja in the series, in ninjutsu he's one of the best, his taijutsu is spectacular, genjutsu he is exceptional, he's fast (both physically and mentally) and he has the brain of a genius. His quick thinking in the last chapter in such conditions says it all really, he's always been a prodigy, not much more can be said.
Minato:
It's hard to really evaluate Minato since he hasn't had nearly enough screen time or shown enough feats. However from what we've seen it is as clear as day that he is a one of a kind genius. Yes he's a one of a kind because despite not belonging to some prestigious clan, not being born with any special ability or being blessed with powerful chakra or kekkei genkai, he's still the definition of a true ninja. Just like Kakashi, minato too is a genius (a prodigy), with great physical and mental prowess. He's definitely wise and knowledgable (most Kages are), he also has the cool demeanour and intelligence. His intelligence has proven on more than one occasion to be one of the greatest in this manga, and his skill as a ninja speaks for itself (he's a Hokage, nuff said).
In comparison:
Minato has little feats compared to Kakashi so it's hard to judge. Minato has only shown a fraction of what he's capable of, his arsenal is small and has still yet to reveal everything up his sleeve. What's great about him however is that he only needs to rely on 2 techniques, basically just 1 technique (FTG) which gets the job done almost 100% of the time. When it comes to intelligence I always used to think Kakashi was the best overall (even Guy said no one was better at analysing than Kakashi) but then I changed my mind when I saw Minato take charge and lead a group of ninja who he hardly knew and utilised their abilities in the best way possible. He analysed Madara's truth seeking balls, figured out it's weakness and determined now to counter it. Something even Kakashi was unable to do, not to mention analysing Onitos kamui only took minato 1 encounter to do, while it took Kakashi, Guy, Killer Bee and Naruto several chapters to do (despite Kakashi possessing the same power, more or less). Despite both having cool demeanours and ability to stay calm in bad situations, both have crumbled when the worst has hit them. Kakashi finding out Obito was still alive and now evil almost broke him, same thing happened to Minato and was unable to fully fathom what his once precious student had become. Which just shows both of them aren't perfect, but they still endured in the end. Although Minato stopped Kakashi killing Obito and may suggest that Minatos will is stronger; the truth is that Kakashi has gone through a lot more than minato so I can't judge Kakashi for almost killing his team mate. Both are inventors of jutsu too I might add, which shows just how much genius they possess.
If I had to pick who is the better all round ninja, then honestly I'd have to say kakashi. Even though I think minato is slightly smarter (by a fraction) and minato is stronger, Kakashi just seems the most well rounded. And the lack of feats doesn't help minato, if we knew more of his abilities then I may have chose differently. The deciding factor is that Kakashi has endured more than anyone else and still continues to fight for what is right.