Weapons are a major factor in the Metroid universe because there are typically only a few different options. Each weapon has it's own unique abilities and features. Unlike so many other first person view games, the weapons in Metroid games actually play a part in puzzle solving as well as combat. In MP and MP2 the weapons system is different from MP3. In the first two games you must use the C-Stick to switch weapons, much like the D-Pad is used for visor switching. In MP3 each weapon upgrade is "stacked" onto the preview weapons so there is no need for switching. This is a nice feature when it comes to battling multiple types of enemies at a time. To add on top of this is the feature that MP3 offers to use the grapple beam to assist in combat, thus, doubling it as a weapon.
Another major advantage to "stacking" weapons is how it effects doors. Doors are opened in Metroid games by shooting them and this is handled in a few different ways in each of the three games. First thing to mention is the fact that MP and MP2 force you to open doors with different types of weapons. This is obnoxious when trying to quickly run through the world because you are constantly switching weapons just to open doors. MP3 limits this issue. In the end though, the weapons really come down to how they are used in each game. The weapons in MP and MP3 are extrememly similar (both have ice, fire, and explosive weapons) and MP2 has very different weapons (light, dark, and combo) but is limited by ammunition. The difference really comes with the utilization of the weapons in each game. And requiring weapon changes to open doors and restricting weapon usage with ammunition are the two major factors.
1) Metroid Prime 3: Corruption (Freeze Missiles and Fire Beam, stacked weapons, Hypermode)
2) Metroid Prime (Fire, Ice, Plasma)
2) Metroid Prime 2: Echoes (Light, Dark - limited ammo)
The upgrades, in all honesty, are really what moves a Metroid game along. Without discovering a new upgrade it would be impossible to progress in the game. Or rather, if you had all the upgrades from the beginning the game would be over extrememly quickly. MP was somewhat limited in upgrades compared to the other two simply because they only had so much they could add in the first 3-D iteration of the franchise. To be honest, there isn't a single upgrade in MP that isn't available in one of the other two. So in terms of sheer numbers, MP is lacking.
MP2 added a few neat additions to the missiles by allowing you to lock onto multiple enemies at a time and adding the Screw Attack, but MP3 upped the ante again by making missiles freeze enemies and objects. Really, MP3 is a compilation of the upgrades from MP and MP2 with a few additional ones. Aside from the Gravity Suit (there was no water in MP3) and Power Bombs, there is nothing that MP3 doesn't offer that the other ones do. MP3 does, howevever, offer up a few new upgrades. There is the use of Samus' ship in combat and puzzles and the use of the Grapple Beam in combat and puzzles. And let's not forget Hypermode, the mode that allows Samus to use Phazon as a weapon.
1) Metroid Prime 3: Corruption
2) Metroid Prime 2: Echoes
3) Metroid Prime