What would I want?
3 playable characters. Not separated storylines, but rather one story where the 3 paths intersect at times but each have their own significance.
And the three characters would be: Prometheus, Pandora, and a new Chosen One.
The Chosen one would be a choice between an angry emo male kid, and a truly psychopathic but extremely hot female. The Bio Metal in question would be Model V (VAVA/Vile.)
In all honesty, having a modified version of Vile's play style from MHX in a ZX game would be orgasmic.
The story is Prometheus and Pandora managed to survive the underwater lab explosion. When they fully regain their minds and abilities, Albert is dead as a door-nail, Ouroboros is sunk. Thomas has fully revealed himself to the world, and the [parasitic bomb] hits the fan. Thomas tricks the world into believing that Aile/Vent and Grey/Ashe are truly evil and had their own plans all along, and a war between the Guardians and Legion ensues. Mikhail barely escapes with his life and defects to the Guardians.
In the current world, thanks to modifications made due to the Equality Laws passed by Thomas and Albert, Reploids under normal circumstances can never reach the level of power and ability that reploids of old did, like X, Zero, Vile, Sigma, etc. However Thomas (as indicated by the secret ending of ZXA) releases the controls that put such limits on Reploids and Modified Humans. Anyone who is on Thomas's side becomes able to become much more powerful.
Prometheus and Pandora are tired of all the conspiracies, and in general all the bull[parasitic bomb] of the world. They wish to destroy the world, not in the physical sense, but rather destroy the most powerful institutions, after which chaos would ensue, and they hope whatever new world is born after that chaos would be better than the current world. Just one problem: They are powerful, but there is no way in hell just the two of them can fight a two-pronged war against both the Guardians and Thomas controlled Legion. It is at this point they come across information that could make their dreams feasible.
A bio-metal has been discovered. This bio-metal is a left over project of Albert's. It would essentially have been the demonic right hand of the New Mega Man King. However, the soul that Albert used to power this bio-metal was highly unstable and did not differentiate between friend and foe. So Albert sealed Model V away.
After the destruction of Ouroborous, which Model V was on, it was discovered by Illegal Raiders, not knowing what it really was, except that it was a bio-metal and therefore could be really valuable. Since the events of ZXA, the Raiders had built a new underground main base. However, upon discovery of its existence, both the Guardians and Legion sent Spec-Ops teams to retreive it.
Meanwhile, a girl in her late teenage years, who had recently escaped from prison. She was wandering around about two days before the Illegal Raider base was attacked. She, with her skills, manages to infiltrate the base. She is about to initiate a plan to kill everyone there for fun, when Raider radar detects both groups. She decides to kill them instead. She manages to snipe and blow up several enemies from both sides, but the large number of spec-ops is too much for her, and she starts to receive injuries, and she starts trying to run.
However, she can't run for long, and is pinned down in a cargo room. With Guardians flooding in from one entrance, and Coalition forces in the other, she is trapped. Since the two opposing forces open fire on each other, this buys her a little bit of time, but she knows the victorious side will come for her soon. That's when she hears a voice.
"This is [acid burst]ing me off! I want to be strong! I want to be free! But I'm a freaking piece of floating metal being fought over like some inanimate weapon!!!"
She looks around.
"Who said that?"
"Whoa, what the hell, you can hear me kid?"
After a conversation I don't feel like typing out, the two Mega Merge. The girl fights her way out of the facility, only to walk into a giant two-pronged ambush. However, Prometheus and Pandora cause massive damage to the ambush party, and manage to teleport her out......
Holy [parasitic bomb], I went way of tangent, and this story would probably never happen. But I can dream.....