That's strange because I consider the transition Metroid made from 2D to 3D one of the best ever. Metroid Prime retains all the aspects of what made Metroid games but in a 3D environment.

Answering the OP's question:

1. Metroid wins for me but I do love the Iga-vanias (I've backed Bloodstained and can't wait to play it!)

2. A close race once again but Super Metroid wins. I love replaying that game from start to finish. Also it's one of the most entertaining games to watch speed runs for.

3. Guacamelee would be on top in the non Metroid or Castlevania category. Ori and the Blind Forest was great too but getting locked out of some areas really didn't go down well with me.

1. Castlevania. On the Metroid side there are like 3 games if we only include de 2D games.  

2. Symphony of the Night. Super Metroid is close though.

3. Clash at Demonhead or Shantae

I wouldn't classify the first 4 Castlevanias as Metroidvanias. Maybe Simon's Quest but definitely not 1,3 and 4.

Well, I only like 2D Metroids, and I haven't played 3D Castlevanias other than 64 and Lament of Innocence.

So, judging by the 2D Games, I would pick Castlevania, since Symphony of the Night is one of my favorite games of all time. Super Metroid is great too, but SotN is a masterpiece.

I disagree. Prime is one of my favorite games of all time, but one of the most fundemental aspects of the Metroid franchise is how agile Samus is and how the level design, boss design, and Samus's moveset are all designed to make the player feel powerful through that growing agility. That's pretty much entirely lost with the Prime games, as Samus is a relatively slow tank in those games, the level design isn't nearly as verticle or platform-dependant, and most of the enemies and bosses are designed to make you strafe to the side, rather than execute a proficient level of platforming. She also looses basic fundamental platforming abilities like the speed boost, wall jump, shinespark, etc. The Prime games are awesome games in their own unique way, but they were designed very differently from 2D Metroid when they didn't need to be.

The only franchises I can think of that transitioned perfectly from 2D to 3D are ones like Mario Kart or F-Zero, but that's not really fair for a multitude of reasons. I also think this new Zelda will be the first time, barring maybe Wind Waker, that the franchise really made a faithful transition into 3D, though I still think the level design in Dark Souls is a more faithful to 2D Zelda than what Zelda U is doing.

And just to bring this back on topic, that's why I don't really like the term "Metroidvania" when describing games inspired by Super Metroid and Castlevania SotN. When I look at Metroid Prime, it doesn't even fit under the same genre for me because it lacks so many core design fundementals that make up what people call "Metroidvania." If you look at those games as "platform adventure" games instead, or games that are designed primerily around the use platforming as an unlock tool for exploration, a game like Prime doesn't really fit that description, even though it does have a little bit of serviceable platforming in it.

I prefer the Castlevania series. I find the style, characters, and music much better in every way. Metroid is a bit too... meh for me. Never been into Metroid like I love Castlevania. Especially Symphony of the Night

Argh, I realize I didn't answer the OP correctly.

1) Metroid, although both have turned out excellent "Metroidvania" games since 1994.
2) Super Metroid, but SoTN is an outstanding game also. My favorite Castlevania is AoS.
3) Guacamelee, Shadow Complex, and Teslagrad

I guess I dont like metroidvania then...