Prime 2 while it has some way too big difficulty spikes (The Spider Guardian... Ugh) at times, it has some of the best boss battles in the Metroid series, has a really fitting atmosphere, and is an amazing experience overall.
Prime 3 is a really good game. Just not as good as Prime 2 in my opinion. It was really easy compared to Prime 1 and Prime 2, and I dislike the story. I prefer the Wiimote control scheme over the Gamecube one the other two games used, though.
So for me Metroid Prime 2 (Trilogy version) > Metroid Prime 2 > Metroid Prime 3
My current Wii U game list:









My current 3DS game list:








