To me that was Zelda. It have a very great and big universe of possibilities.

From a story standpoint, it's quite easy to explain, you've left some of the most important details out.

First off, Adam (or the computer, as it were for the first part of the game) makes sense. The mission that the Federation sends her on is to follow the orders of the computer, which Samus notes in the opening cutscene (and perhaps somewhat telling is how reluctant she is to do so). That contrasts completely with deciding to follow the orders of someone for no real reason other than "gee I kinda miss Adam."

The upgrade system makes sense as well; the computer notes on several ocassions that the downgrades take time to finish. Once they're finished, they're sent to Samus immediately; presumably the more powerful ones take longer to make, which is why you get them later. Regardless, this isn't Samus choosing to not use life saving equipment just because someone says she can't; as opposed to Other M, where Adam forces Samus to run through the majority of a super heated sector without the Varia Suit because of reasons.

Fusion's definitely more linear or "action based" than previous titles, which is a sticking point for some, but it isn't for me because there's still very much an element of exploration to Fusion. While you're usually unable to get outside of a sector once you step inside, the sector is still very open and explorable and there's plenty of room for player discovery. Other M, on the other hand, is so linear that it makes Fusion look like something out of MC Escher. There's one strict path to the goal that you cannot diverge from whatsoever until the very end of the game, and the sectors themselves are incredibly straightforward with no room for any exploration. 

I don't think anyone complains about stacking beam upgrades, but it'd be hard for them to like Fusion if they did.

And, finally, the big two differences from Fusion to Other M: Samus isn't an absolute wimp, and the story isn't incredibly stupid. Fusion's story is by no means an outstanding piece of literary work, but it was certainly attention grabbing, resolved all of its main plot points, and most importantly, gave a well thought out, well reasoned, and engrossing reason for Samus to go hunting again. Other M fails on all three of these levels.

I agree. Prime Hunters takes the show. In my list of personal favorites. 

10. Prime Hunters

9. Metroid 2

8. Metroid Other M

7. Metroid

6. Metroid Fusion

5. Metroid Prime 3

4. Metroid Zero Mission

3. Metroid Prime 2

2. Super Metroid

1. Metroid Prime