Normally when you think of making a deathmatch in a fps you may decide to design the levels around gathering weapons. But I felt this conflicted with what Metroid and really Samus' abilities were about. Think of designing Metroid Prime 3's deathmatches in two different categories. Designing more traditional fps levels and designing levels that could essentially be ripped and placed into a multiplayer Zelda adventure. Should the progression of the deathmatch be determined by gaining special items in adition to your present abilities (like a lightning sword or gravity gun allowing you to move anything including yourself). So you would pick your character based on what abilities you want. Samus would keep her abilities from the game and the same would apply to other sentient aliens, marines, and boss characters. Rather than focusing it on everyone having to be Samus so you can rush to upgrade your suit, I would like to see Samus' suit's individualistic properties shine on there own against players that don't have her technology. I mean imagine if you had to design the deathmatch around Master Cheif versus Samus. Upgrades for Samus' suit wouldn't work for Master Cheif and he would promptly be dead. Instead the level would be more balanced if Master Cheif and Samus each had their own abilities from the beginning of the match but who gains the upper hand should be determined by whether you pick up the sword or needler (or if youre Master Cheif, both), etc. This is all hypothetical for the purpose of giving an example since Bungie rolls with MS right now.
Part of completing the multiplayer trifectum is that there must be an aspect of coop. I would prefer four player coop next gen, you can always just play through on two player too online, offline, or both. Metroid would be a hard game to turn into a counter op game, but it could be done I believe via the internet. Imagine playing a game where every alien you encounter is controlled by another human player somewhere out there in internet land. Imagine getting to play as the bosses against someone else playing as Samus.
I want to see a balance between the characters (not too gimicky though) in deathmatch and coop modes so that everyone does not have to be Samus or at least wear a suit like hers. You could insert into the story line for coop three other individualistic suits Samus has on her ship that three other players can wear to join in at any time.
I would like to see alien technologies as advanced as Samus'. Instead of having every character being able to ball up like Samus in the new DS game; some alien enemies may have floating orb counter parts (like the fairies in Zelda or R2D2 in Star Wars). The orb/bot could be sent out and controlled by the player like the bots you could control in PD on N64. It could do most anything Samus could do and go into small areas. It could act like a helper or protector during battle floating behind the character (you could even use the robot's point of view and visor modes throughout the whole game while controlling the character in third person view via the bot's first person perspective). Perhaps the floating bot and the character are linked, so you have two sets of eyes. It really would play off the question of who is controlling who here.