I certainly hope so. I don't mind the Prime 1 and 2's controls, but dual analog controls are simply more fluid and less cumbersome. The Switch also has more buttons than a GameCube controller (clickable sticks and an extra shoulder button), so the developers have more options control-wise than Retro did with the GameCube titles.
I would not mind seeing an option for the original controls, however; people who are not experienced with first person games may find dual analog controls daunting, and the original games' control scheme was a big strength in that regard. All movement and aiming was handled entirely on one stick (with the latter needing the assistance of a button press), meaning that it was very simple to control even for the uninitiated. I definitely think that such a thing should be an option for accessibility.
As for prospective Prime 3/Trilogy-style controls... I would love that, but without an IR reference point like what we had with the Wii, I can't imagine it would be too accurate. Plus, holding the right Joycon upside down not only feels a little awkward, but completely cuts off access to a trigger and shoulder button - while also making the face buttons harder to reach. If aiming is completely gyro-based, on the other hand, then it would get very tedious to constantly re-center the aiming, especially for a first person title. Gyro-assisted aiming would be a superior option, IMO.