It's one of those things. When Metal Gear Solid 2: Sons of Liberty came out, it was divisive because of Raiden's inclusion. Plus, the Big Shell was a bit of a bland backdrop. Over time, people looked beyond the disagreements and found a good sequel to the first game.
In Metroid Prime 4's case, there are some staunch anti-Nintendo folks that will be angry with the final product no matter what. There will be people that feel Retro Studios isn't the company they were when even Metroid Prime 3 came out. There are those that dislike modern gaming as a whole and dislike any sequel/remake of an older series. Everyone is coming from a different viewpoint and level of dedication.
It all comes down to if you find the game fun and if you think the game is a worthy successor to the previous trilogy. You will have to argue your case, but it helps not to be emotional. You'll have to fend off users being emotional themselves, and you'll have to be ready to accept counterpoints and ask if they're valid. Think of argumentation as a sport more than life or de*th.
TL;DR: It's just video games.