I just watched Mac Zero and Shin Kudo wasn't all that good; he was good, yes, instinctive, yes, but he never learned to 'feel' his opponents, nor did he ever get good enough to down an SV-51... I guess he figured it out before he folded to the center of the galaxy, but still.
Hikaru was a great pilot and all and maybe surpassed Focker but I'm going to have to say that Isamu Dyson may well top the list, pushing the YF-19 to its absolute limits.
There are other variables to consider though. All things equal, would Alto Saotome be as good as Hikaru Ichijo in a VF-1X?
We probably won't ever know that answer, but I am going to agree here that Maximillian Jenius is probably the single best (most talented) pilot in Macross history.
Frankly, I think Basara Nekki would be a terrible combat pilot, because much like Hikaru in his early days, I think he'd have trouble pulling the trigger when face to face with an enemy.