There are plenty of horror elements in the Prime trilogy.

Metroid Prime 2 is probably the most atmospheric and "creepy" game of the entire franchise. Besides, Echoes has the most references to Alien thus far: 

• The idea of the main planet having a turbulent atmosphere which damages the protaganist's ship is a concept which also appears in Alien when the Nostromo is damaged while landing on LV-426 and has to stay on the planetoid until repairs are complete.
• Samus being sent to Aether to restore contact with the troopers is another concept in Aliens in which Ripley and the Colonial Marines are sent to restore contact with the colony on LV-426.
• The Splinter hive in the Federation Troopers' Ops base and the discovery of the dead troopers caught in webs is similar to the discovery of the Alien hive and cocooned colonists in the colony complex in Aliens.
• The scene where Dark Samus aims at the real Samus when they first meet is, according to storyboards, based on the climax of Aliens.
• The Federation Troopers can be considered similar to the Colonial Marines from Aliens.
• The part where Splinters manage to get on board the Tyr and damage it beyond repair is similar to the scene in Aliens where an Alien boards the first Sulaco dropship and kills the pilots, causing it to crash, stranding the remaining survivors.
• One of the deceased Marines, PFC G. Haley, is described to have lost his sanity during the Splinter attack. This is similar to Hudson, one of the characters from Aliens, who also loses his sanity when all hope of surviving the mission on LV-426 is lost.

Even in Metroid Prime 3 we have the abandonned spaceship Valhalla that was the victim of a space pirate attack. In the ship lurk all kinds of phazon enhanced creatures and the bodies of the victims (both marines and space pirates) tell brutal stories. The metroids leaving behind empty shells of bodies that desintegrate on touch was also a nice addition.

Super Metroid is also arguably the best Metroid game. Everything was bad in Other M. Other M shouldn't ever be used as an example for anything in Metroid. Look at 3D Mario, or literally any successful 3D platformer, since that is half of what the Metroid franchise is based on. Linear platforming. That's how 3D Metroid should be, and that is completely lacking in the Prime Trilogy.

3rd Person doesn't ruin anything. It didn't ruin the immersion in and of the 2D Metroid games, and adding a 3rd dimention doesn't somehow change that. And it definitely wasn't the reason Other M was bad. Metroid is a 3rd person franchise, and the Prime trilogy's jump into 1st person added nothing and took out many things. Nothing you do in the 1st person in that game gains anything from switching to the first person, aside from debatably the Scan Visor. In that case, a Metroid game could simply put you in first person when using it, just like how you're put into first person whenever you're using the Morph Ball. Or they could just let you scan things in the 3rd person. All the combat visors gain nothing from being in the 1st person, and could just be done in the 3rd person.