While the stealth mechanic would be great for the Metroid series to develop (Metroid Zero Mission being the last one to do something to the effect in 2D, and then the Morph Ball being the proxy for such gimmicks in the Prime games), I highly doubt Nintendo will be innovative enough to give the fans what they want in these terms. As such, I fear that the most we'd get in terms of stealth-like sequences, would be limited to what we had received in the beginning portion of Metroid Prime 3 Corruption's Pirate Homeworld level: Morph Balling under the floors of the Pirates, sneaking across a room that was just made vacant by all Pirates, and dropping through ventilation shafts. And then being uncovered by cutscene, blowing your cover and turning it back into an assault mission.
As for controls, well...
Nintendo Labo Arm Cannon props, anyone?
But seriously, the motion controls might receive more treatment similar to the New Motion Control upgrade that MP1 and Echoes received. However, I do easily see the Grapple Lasso being brought back, and perhaps with more control, since both Left and Right Joycons have gyroscopic controls that could be utilized.
Also also, Aeion. Let's just see.
What I'm mostly concerned about is timeline placement. We have yet to have a true bridge between the Prime series and Metroid 2 (now Samus Returns), but MP4 might help provide that. In the prologue to Samus Returns, the Federation council deem it necessary to order the genocide of the Metroid race, sending scientists, then soldiers, to SR388. It's possible that the Federation might be involved in the narrative within MP4, since the council thinks that it's enough for them to send scientists to destroy the Metroids. Perhaps Samus helps train soldiers and/or scientists in how to dispatch of Metroids?
Maybe, if Sylux taking the Metroid from Fed Force is any indication as to the story of MP4, then the progression of the story should lead to that inevitable conclusion: the Metroids are too dangerous to leave alive on SR388, and they must be destroyed. And this elite team of scientists is enough to eliminate them. (Also, soldiers sent later to supplement and rescue those scientists.) And if both of those options fail, there's Samus.