I don't think Goku will always be stronger than Vegeta now; though it's hard to pinpoint exactly how equal they are, I think the gap has closed quite a bit in Super. Vegeta has always been a better tactician (when he's not letting androids get absorbed
), and a genius when it comes to fighting.
In DBZ,
Goku always trained to get stronger to protect his friends and comrades, which I believe may have put him a few steps ahead of Vegeta since his intentions were always pure and he had no personal grudge against him so he could focus more. Vegeta on the other hand would strive to be stronger simply to surpass Goku and get a one-up on him, an obsession which I feel blinded and prevented him from reaching his true potential.
When you fight to protect something you love and hold dear to you, the hunger to become stronger comes natural. Doing so out of obsession will only get you so far and Vegeta has changed that now I feel.
Goku if anything is starting to regress as a character, while Vegeta is growing and improving. Goku's always been a bit of a dumb ass and that's one of the qualities that makes him so lovable - it's just that they've made him so dumb now it's almost like he's become the TFS version of himself dumb.
I mean having to be told by by someone else (Vegeta) that his opponent (G Freeza) is running out of ki, yet on Namek he was able to spot that weakness with Freeza with no problem as a SSJ.
I'm surprised Goku even passed the test in the tournament to be honest.