The Metroidvania has always been a popular genre among indie game developers. However, more often than not independently developed Metroidvanias too closely resemble Metroid. Indie games like Xeodrifter and Axiom Verge both try their best to not only emulate the mechanics of Metroid but also its aesthetics.
Iconoclasts, on the other hand, has a very different aesthetic from Metroid and even though it has similar game mechanics there are differences that make it unique. Please bear in mind my impressions of Iconoclasts are based on promotional trailers and the playable alpha released in 2012.
Emphasis on Narrative
One thing that separates Iconoclasts from Metroid is the emphasis on narrative delivered through dialogue with NPCs. Iconoclasts is set in a world that is governed by the militaristic religion One Concern. You play as a young mechanic named Robin that often helps people by repairing their machines. However, Robin is an unauthorized mechanic and in the eyes of One Concern being unauthorized is a sin.
The world of Iconoclasts is one of science fiction like Metroid but has a completely different feel. Instead of invoking feelings of isolation with alien planets like Metroid, Iconoclasts has a more playful tone with the vibrant visuals of mother nature. While Iconoclasts is a Metroidvania it is very linear in structure with event triggers that push the narrative forward and environments that generally move in one direction.
Combat and Puzzles
The introduction of melee combat itself makes fighting in Iconoclasts very different from Metroid. The game does start you off with a stun gun but it is very weak compared to the wrench. What I really like about the stun gun is the aim assist that makes it possible to shoot enemies diagonally without moving. The wrench and gun in Iconoclasts are not only used for combat but also for puzzle solving and exploration.
I prefer the puzzles in Iconoclasts to those in the Metroid games because instead of being about using the right thing in the right place they're about timing and execution. These more "active" puzzles in Iconoclasts make the puzzle solving feel less detached from the rest of the experience. Even the boss battles are a nice mix of both reflex challenge and puzzle solving similar to the The Legend of Zelda series.
Hopefully, more indie developers will follow Iconoclasts' example and make Metroidvanias that don't only pay homage to the Metroid series but also deliver their own unique experience. Iconoclasts is being developed single-handedly by Joakim Sandberg and is set to release on PC and PS4 this year.
While you're waiting for Iconoclasts you can check out Joakim Sandberg's first commercial game Noitu Love: Devolution which is getting a port to the Wii U and 3DS in September. So if you're bummed about Metroid Prime: Federation Force you can play Iconoclasts to celebrate the 30th anniversary of Metroid.