Puzzles and Level Design
One major factor of the Metroid series is the puzzles. There are a few different types of puzzles typically in the form of first-person view, morph ball, and bosses. I will be touching on bosses later this week so today I will only be discussing the other two types. All three Metroid games in the trilogy sport the Spider Ball, an upgrade that allows you to stick to walls on a pre-determined track, but only MP2 and MP3 added the Boost Ball feature to allow large jumps between tracks. So in regards to morph ball puzzles that feature alone added more creative morph ball puzzles to the later two games.
In regards to first-person view, it really comes down to the different visor and weapon options and the overall level design of each game. Depending on the visor and weapon combinations you have there will be different puzzles. The X-Ray Visor coupled with the Nova Beam in MP3 allowed some neat situations because it allowed you to see and shoot through objects. The Light/Dark World level design in MP2 turned out not to be the best fit for the Metroid series. In a game that often requires you to revisit areas multiple times it is often very difficult keeping track of multiple rooms twice (one for each world).
1) Metroid Prime 3: Corruption (Boost and Spider Ball, no Light/Dark)
2) Metroid Prime 2: Echoes (Boost and Spider Ball)
3) Metroid Prime
This should be a pretty obvious one considering the core gameplay and visual mechanics remained the same in all three Metroid games. When MP first came out there was some fear from the Metroid fanbase that the transition from 2D to 3D wouldn't be so smooth. Since the release of MP there have been three Metroid Prime games released (counting Metroid Prime Hunters for the DS) so the fans were definitely pleased. Everything from the edges of the visor being visible to the drops of rain that hit Samus' visor, the fans were impressed. The transition from Super Metroid to Metroid Prime has been compared to the Legend of Zelda: Link to the Past to Ocarina of Time transition. It is that good.
MP2 was also a splendid game but, in the originality department, failed to make any real impact. In fact, the whole Light/Dark World could be regarded as a step back in originality if you look at Link to the Past released for the Super Nintendo. There were new features, weapons, and visors but there wasn't anything quite as ground breaking as the brand new control scheme or the new motion controls found in MP3.
1) Metroid Prime
2) Metroid Prime 3: Corruption
3) Metroid Prime 2: Echoes