Trust me folks, it's not like NoA is blind to the fact that almost every time they get interviewed about bringing old IPs back, Mother is always on top of the list. The problem with a series like Mother is when the rights for various parts of the game belong to other people (read: Itoi) it can get pretty sticky if they want some atrocious fee or insane conditions.
To use an anime as an example: When Funimation announced it was bringing Kodomo no Omocha to America (something anime fans had been clamoring for maybe 12 years or so... like Mother as it were...) they were immensely excited. However a few months before the release, they found out that the company that they bought the rights to the show from did NOT own the rights to the opening song. In a very unusual case, the singer held the rights to his own song, and wanted an astronomical amount of money for it. As a result, when they released the show in America, they had to remove the song altogether. This doesn't seem bad in and of itself at first, but if you watch the show in Japanese, the song literally fills the first 7 or so episodes and there's even a cameo from the singer himself. What happens, due to rights, is they had to botch the audio here, so these bits are played in complete silence while the subtitles keep rolling. Fans were very upset, and while some people were very understanding of Funimation's predicament, many others thought they were just making excuses.
This could be a very similar situation, and perhaps NoA does not want to speak about it because it would seem like they were making excuses. In addition, NoA saying things about Itoi could hurt his relationship with NoJ, and I don't think they want that. NoJ could be telling NoA to keep it's damn mouth shut on the topic for that very reason.
Do I know any of this for fact? No, it's speculation. But seeing everything that's happened, interviews, and rights related points has led me to believe there's more to this issue than Nintendo "hating gamers"