Here's a quote he's credited with by
http://www.totalvideogames.com/news/Itagaki_Ninja_Gaiden_2_Is_My_Final_Instalment_13219_7010_0.htm"It was a weird chimera of a game, with some things here and some things there. From a game design standpoint, I don't think it was done well at all. This [Ninja Gaiden II] is the definitive version of Ninja Gaiden...I look at NG2 and I think it's the culmination of everything I've done, but it's also a chance for me to change how I think about game design."
That is essentially saying whoever designed the game system (controls and such), did it poorly. Since he had nothing to do with it, he can see the flaws and differences in how he would have done it. It's not really an insult on the members of the team, they just do what they;re told, it's whoever took over his place. Itagaki is a Game Director, in charge of creative aspects of the game. He was insulting the creative direction the game took, not the team of people (he would probably agree that the higher quality graphics are nice, and that the ideas that were used were decently executed, but just because a game looks nice, and the changes are done "well" per se, doesn't mean that the game itself is good.)
An example would be my view of FF8. Sure, it has great graphics, and the GF system is well done, but I still don't like the game at all, and think the story is rather stupid. Doesn't change that the game was well put together, I'm insulting the guys in charge of the creative part.