You do realize Goku was holding back the entire time with Majin Vegeta, right? And that Vegeta figured this out?
He could have went SSJ3 but chose not to because he had never used it in a real fight before, thus he didn't know how to use it to his advantage in a fight
Also, SSJ3 had a severe ki consumption problem, so Goku wouldn't have been able to fight at full strength for very long, anyway, so he had to stay SSJ2 in order to keep pace with Vegeta
So if anything, him going SSJ2 at the time could have been to the benefit of Vegeta as he would be closer to becoming an SSJ3; since both of them trained rigorously over the 7 years that had passed since Cell was defeated, there's a chance both of them could have unlocked SSJ3 at the same time, therefore they would both be on equal terms in terms of strength
And also, Future Trunks got killed after Gohan went SSJ2/Android 16 got killed