Him saying "I can't maintain it for long" doesn't mean anything unless we know who he's being compared to, maybe Minato just has very high expectations for himself and maintaining it for five minutes it considered bad to him, who knows.
It doesn't change that he literally just blinks and is suddenly a perfect Sage, which is just as good if not better than Naruto during the Pain Arc.
Anyway, all this is predicated on the assumption that Fukasaku was talking about Naruto surpassing them in Sage Mode as oppose to in general, but I don't see why that wouldn't have been specified if it was the case, instead we get a general statement about him surpassing them.