So I just started designing some aspects a current project I've recently started and as I work on it at times I feel I'm walking a too far into one of my games inspirations, metroid. The idea of the game is sci-fi action/platformer much like metroid, but trying to get feeling of something bigger than what metroids story does. the protagonist wears a prototype military suit that along with his main weapon is able to be outfitted with the choice of three subweapons that are implemented into the armor. Of course the beggining of the game only has one of the weapons unlocked(as it stands of course, much is bound to change as I continue).

To make a better picture of what I plan is that players unlock different subweapons (shotguns, grenade launchers, energy weapons, etc.) based by obtaining schematics/paying research to outfit these into the armor. Under the subweapons different ammunition types(some of which deal certain types of elemental damage that add upon the base damage and I'll get into this later) are unlocked in a similar fashion. I also want to implement a weapon upgrade system as well (but the upgrades are to the ammunition types not the subweapon type). I was inspired by the upgrade system and subweapons via Megaman Legends.

Now certain ammunition types will deal additional elemental damage and enemies can be categorized into types(such as armored or flesh, etc) that are strong, weak, and netural to certain elements which hopefully can add a little strategy to players choosing their weapons and upgrades. Overall I like the idea of it all but sometimes my overall concept feel like I'm sticking to close to some of my inspirations.

Does it seem my characters design is too close to Samus/Megaman. I feel the weapon design may be closer towards megaman (especially legends though the subweapons are different enough from legends I think it justifies it). Thoughts and opinions would be great and I'm willing to share more if anything is confusing (I know some might be, a lot is going through my head at the moment).

It sounds similar, but the details you've given seem vague enough that you could make twenty games fitting that description and each one be distinctly different.

If you are worried your mechanics are too similar, I'd just compensate by ensuring other areas of the game are distinctly different.

You could make the visuals feel alot different than Metroid, and make the methods and means of exploration alot different then Metroid.

You could make the player movement feel different than Samus' movement. Samus is fast, acrobatic, and flexible: a sci-fi Sonic the Hedgehog. You could make your suit heavy and bulky, even if your character moves fast, and you can play it as a strength of your game design and use it to inspire other ideas for your game: Like maybe your character has to sometimes get out of his suit to reach certain areas, but is now much weaker (with only a sidearm) than when in his 300 lb super-armor. (Learn more toward, and beyond, Halo's Mjolnir armor than Samus')

You could ensure that in no way do you use your weapons as keys to "gate" exploration of your world (since Metroid does that heavily). Instead, maybe key the world through events or actual keycards.

You could ensure your plot, though sci-fi, isn't related to Metroid's, and your backplot for the main character doesn't resemble Metroid.

What does your game 'feel' like? If it 'feels' like Metroid, even if the plot is different and the visuals are different, and the mechanics are different, people will claim it's a Metroid clone. If it doesn't 'feel' like Metroid, even if the plot is the same and the visuals are the same and the mechanics are the same, people won't subconsciously think of it as a Metroid clone, even if it is one (Though they may realize it when they take a step back and consider).

Interesting take on that, I appreciate the input, it gave me quite a few ideas how to change some of the exploration aspects and feel of the character compared to Samus. I can assure the overall plot is nothing like metroid, so I feel much better that people may not intstinctivly say "this is just a metroid clone" but rather hopefully they will see it it's more of just a metroidvani styled game with it's own unique feel to it.