IGA talked about hsi past production issues with Konami. For example, he actually would like to focus more on the handhelds then the console games because they are 2D in nature, but keeps getting nodged towards trying to improve the console games. Something has had mixed results. He also says he doesn't exactly get a good budget like lots of other projects such as MGS. It's part of the reason why they have to keep recycling many of the sprites through out the games.
IGA doesn't deserve the full blame for the success and failures of the franchise, it's still a product owned by Konami and it's staff, and in the end all he has is a good deal of power over it, but even Konami can overide them or simply time and budget problems can get in the way too.
If you want a good example, look at the Original Director of FFXII That guy is one of my favorite videogame directors, but he got royaly screwed over by Square-Enix on many points. If it weren't for that Basch would of been the lead in the game and Vaan would of just been another anoying sidekick instead of the annoying main lead.