I've beaten every 2D Metroid and Metroid-Style Castlevania. Here are my thoughts.
BASIC GAMEPLAY: METROID. Samus' abilities are more fun to use (Morph Ball, Space Jump, Grapple Beam, I could go on), and they allow her to interact with environments in fun ways. She's basically "Spider-man in space." Aside from SotN, CVs are grounded in basic platforming/attack abilities--although I do enjoy their RPG and "Soul Ability" concepts.
BOSSES: METROID. Metroid bosses are generally more creative in terms of design and battle tactics. CV bosses are typically oversized monsters that need to be hit anywhere on their bodies until they die.
LEVEL DESIGN: METROID. Again, Samus' unique abilities allow for more dynamic level design. Metroid tends to have considerably better platforming variety and environmental hazards.
MUSIC: CASTLEVANIA. This is where Castlevania wins decisively, although Metroid is no slouch in this area.
ATMOSPHERE: METROID. Not even close. Super Metroid and Samus Returns both create an amazing sense of dread and claustrophobia through their visuals, music, and level design. Even the original Metroid II has a keen sense of loneliness. SotN is the only CV that feels truly immersive, along with maaaybe CotM.
DIFFICULTY: CASTLEVANIA. Metroids tend to be cakewalks (aside from Samus Returns and the NES original), whereas Castlevanias offer more of a challenge, especially Order of Ecclesia and Circle of the Moon.
STORY: METROID. Neither series excels here, but I give the nod to Metroid because Samus' journey always feels like it has ongoing purpose, not to mention the occasional emotional moment (finding the baby Metroid, the Mother Brain battle in Super). Castlevania is almost always, "Whelp, gotta kill Dracula again."
So yeah, Metroid wins in most categories. That said, I love the Iga-made Castlevanias. Here's my biased ranking/tier list of every game:
Super Metroid Symphony of the Night - Samus Returns (3DS) Zero Mission Order of Eccelsia Circle of the Moon - Dawn of Sorrow AM2R Fusion Portrait of Ruin - Return of Samus (GB) Aria of Sorrow Harmony of Dissonance - Metroid (NES)