To be honest, in all the interviews I've seen or read, I don't recall Paul trying to take a lot of credit for Jon's work. If anything, it seems that Jon is all too willing to give credit to Paul for making Savatage as great as it was, while Paul never stops praising Jon's genius and talents. This is really apparent in the video interviews they did for the Wacken 2015 show, where they are constantly complimenting each other and talking about how the other guy is the true mastermind behind Savatage.
https://www.youtube.com/watch?v=UCXxnUOfcSohttps://www.youtube.com/watch?v=jzURoR13oYsUltimately, I think that they complimented each other perfectly and each brought something to Savatage that the other lacked. Jon is an immensely talented multi-instrumentalist and one of the most brilliant songwriters in the history of rock, but I don't think he ever had a good idea for the "big picture" of how a Savatage album should sound. If you listen to the pre-O'Neill records or the JOP records (which are basically Savatage albums in all but name), it's clear that Jon can write great songs as easily a bodily function but the records from the O'Neill-era clearly have a much more cohesive and well thought-out structure, not to mention amazing, if occasionally a bit obtuse, storylines (and, tellingly, Jon never attempted a rock opera without Paul). By contrast Paul was a guy just bursting with awesome creative ideas and has the vision to know how to bring those dreams into reality, but it seems like he needed someone else with the musical and compositional talent to make it happen.
Really, I think one of the greatest gifts the metal gods ever granted us was getting those two minds together to make some of the best albums that have ever been released. Were it not for the untimely passing of Criss, we can only imagine how far Savatage may have gone with such genius at the helm.