AlphaDream has more autonomy, so it's fair to hold them responsible for trust. But Intelligent Systems cannot be blamed for trust issue and mistakes. It's the higher ups in Nintendo, like Miyamoto, that are responsible for the restrictions.
- What we do know is that AlphaDream fights back against Nintendo higher ups when restricted, and has more autonomy:
- And Intelligent Systems on the other hand, gives in and obeys the Nintendo higher ups when restricted:
- Color Splash: "Mario is not an IP that I created. From the position of someone borrowing the IP, I think its only natural to show respect to the person who created it, and let that feeling of respect guide us. So when Miyamoto-san, the father of Mario, asks us could you make a game with only characters from the Mario family?, I think its only natural for us to give it our best shot. In other words, we are not currently thinking about returning to old NPCs. Incidentally, I do think Color Splash may have proven that we can still make a game entertaining, even if our original characters dont appear as NPCs. And with that belief, we will keep on continuing to do our best." -Tanabe, http://www.gameinformer.com/b/features/archive/2016/12/28/afterwords-paper-mario-color-splash.aspx
Repression of story and original characters remains present in Paper Mario as Intelligent System submits to higher ups restrictions. But AlphaDream seemed to fight back and has since gained a lot more autonomy from Nintendo higher ups. So it's not so much about trusting the devs, the higher ups are typically the ones responsible.