It is a bit stupid to talk about a Metroid game being the "worst", when in general terms as a series they're leaps and bounds ahead and away from any other adventure game.

Oh and for more proof on how Retro dislike sequence breaking, try comparing a copy of Metroid Prime NTSC/U, PAL and then a Player's Choice of any region.

All the tricks are there in Prime NTSC/U, several were removed for PAL (Like the Scan Dash and Track Jump, PAL users had to do a Triple Bomb Jump to get the Ice Beam early).

Now look at Player's Choice, it's basically like they went through Metroid2002 and just REMOVED EVERY SINGLE POSSIBLE CHANCE OF SEQUENCE BREAKING THAT HAD BEEN DISCOVERED.

Seriously, pretty much all gone.

Prime 2, while not having so many small sequence breaking opportunities, has some glaringly huge ones, like completely skipping out the Dark Suit and Amorbis (heck, to complete the game you don't even need to return Energy to Agon, only Torvus and Sanctuary).

Anyway, probably Zero Mission.

Actually now I think about it, Zero Mission actually PROMOTES sequence breaking, since you get different endings for finishing the game quickly on lower percentages, I believe lower than 14 or 15%, which requires you to skip out a number of key items.

That said, Fusion gave the opportunity for the 1% game, which was quite a challenge.

Eh, I'd go for Zero Mission.