It really depends, Castlevania is more sided with the medieval fantastic style, with references to many things written on books, movies, and partly historical references, Metroid is a scifi action platformer game at it's core, with elements of the movie "Alien", comparing those two is quite hard to say, you can't compare the Metroid Prime Trilogy with any of the Castlevania games nor the original Castlevania trilogy with the first Metroid.
The only real fair comparison there are between the two is something along the lines of "Super Metroid" and "Symphony of the Night" but that's quite hard to compare, while both have similar map designs and navigation, Super Metroid is a shorter but at the same time an immersive, intriguing game, SOTN is all about cutting demons, and you feel like you're into a fantastic realm where many things happens, you catch my drift?.
Comparing Castlevania with Metroid is like comparing a Fairy Tale (In a certain sense) with a sci-fi book, and since i don't have favorites over others, i can't say too much about those aspects either, I frickin' love Metroid, the manga is really fucking good, the important games are really fucking good, and it's just a solid series overall, while Other M is arguably a bad or a good game, for everyone's else is a decent game.
Castlevania is just in the spot that is not going to receive any new games anytime soon, specially considering Konami's stance in actual gaming, we have seen how they turned this series now into a Pachinko profit machine, and with the games is kinda... interesting, the first six games (Including Castlevania 1, Castlevania 2, Castlevania 3, Super Castlevania, Castlevania Rondo of Blood and Castlevania Legends) all of them are linear straight forward games with the only purpose on defeating the evil lord Dracula.
SOTN take the route with the same plot but in a different style, instead of going to level through level, the game focused more on exploring each part of the castle (Still with the only purpose of defeating Dracula, but still), with that concept in mind new games with that style were created for both the NDS and the GBA.
Then we have the 3D Castlevania games, whose best examples are probably Curse of Darkness and probably Lords of Shadow, they appeared for the Wii (If we take Castlevania: Judgement in the formula), N64, PS2 and PS3, with the latter ones being basically a "Godvania" where the game is pretty similar to those from God of War.
Now you see, Castlevania has 3 concepts of games, one for the 2D Linear, one for the 2D Non Linear, and one for the 3D games, going back to Metroid, the amount of titles isn't nearly as huge as the Castlevania games, but most of them were consistent in quality, for example, the 3D Metroid games (Like the Metroid Prime Trilogy) are considered among the best videogames ever created, and one of the best ways to tell a story through a videogame, but also taking account all the good elements in good shape from the 2D Metroids to the 3D games.
All of the 2D Metroid Games are fantastic, which is something Castlevania can't share cough cough Castlevania Adventure cough cough (Even though i love the soundtrack of this game), but while there are awesome 2D Metroid games, the only "bad" one (by fan words) is Metroid Other M, which is still a discussing matter between the fans of the series, right now the Metroid fans are down because Federation Force wasn't the game they wanted, and they were apparently pissed off with that.
And Castlevania fans, while they do know that having a new game is as possible as receiving Gold Orichalcum from the sky, with the new Igarashi game called "Bloodstained" coming in 2017, and sharing similarities with the best of the best, this new game satisfied all of those that won't receive a new Castlevania game in years.
So there you have it, in a nutshell, Metroid games are handled by a good company who genuinely cares about it's fanbase and they try to do everything they can in order to satisfy their audience, they may commit mistakes, lots of them, but Nintendo is still the nice part of the videogames in a certain way, and their quality and experience can't be underestimated, which is a major point in this debate.
Castlevania is handled by a horrible company (And this is not my opinion, this is a fact right now), who doesn't seem to care about the franchise except for Pachinko machines, who knows if in a future they may change for good and finally starts to make games for their franchises (or at least sell the unused ones you greedy Konami fucks).
So in conclusion, i don't have a favorite to pick, they are so different yet so brilliant that picking one isn't in my principles, at the end, no matter how much you look, you can't really compare these two games in the most depth ways possible, since the similarities are quite and between (If we take out the Metroidvania part) so it comes down to one single thing, the Player, if he/she decides to stay with Metroid good for them, if he/she decides to stay with Castlevania, another good for them, if the player decides to stay with both, they decided for the better option
