Would prefer a Multi-Player experience as opposed to another adventure. I think Samus has been fleshed out sufficiently for the time being, however there is a lot in the universe itself to grab a hold of.
I think playing as G.F.C cadet and rising through the ranks on real time battlefields (feels like a real battle, as opposed to just the actions of a linear scope). Given the universe, your own personal cadet (or whatever rank you are) can move and fight according to how you customise them.
Rather than playing specific start to finish, you'll have an Objective Log that updates accordingly, and you can either choose to take on that objective, or dismiss it as unimportant and focus either on your frontlines or other objectives.
There'd also be A.I. team mates to give a general layout of where is what on the field, like where the current frontlines are, supply points, main base etc. They'd move accordingly to the situation.
The game also intends to throw on you adversities the more successful you get as a team. Things from falling aircraft wrecks cutting of supply lines or damaging a whole unit, to enemies ambushing you way behind your lines. In a way, you might find yourself forced to go as far back as alleged safe zones to assist or eliminate.
In a real battlefield, unexpected stuff happens. Expect giant earthworms shredding through both sides of the fight. Take advantage of A.I. efforts as they appear (like some of them decide suddenly to use shields to push a front, support that).
To keep with the Metroid feel, you'd be able to customise your own morph powers. Might be anything from turning into the morph ball to turning into a high powered turret. Or something weird yet assisting like that.
After battle, you'll get a very in depth assessment of what you did and get rewarded accordingly. Rewards could be both war money and items, of which you could use both to buy and upgrade your character. Those materials won't be as extreme in finding or using like Monster Hunter for example, more or less simply 10 different goods that get shared across nearly everything, but you need a lot of them. Something like needing 60 flux capacitors for a Neon Beam, 220 for a Gravity Suit and 30,000 for a DMC Delorean.
To be nice, you start of with a small capacity to do pretty much everything, but the more you do it, the stronger your ability to do it becomes. That could become a deciding factor in who does what with regards to multiple objectives.
As for activating objectives, you go to a rally point. Accepting the objective means you'll have mic priority set to the group doing the same functions, and then you'll proceed with the group to complete that. There's a limited number for different objective though. You wouldn't want 20 people doing an infiltration deep in the enemy lines.
For transport, there'd be regular transport services that change according to the battle. After the first person goes on, there'll be a time limit on the big carrier types for everyone to get on. After that, the remainder spots will be taken by any available A.I. There'd also be other smaller transports you can control. You might find other ways with morph powers.
Sounds like a lot. Sounds like fun. Sounds like a hook to me.
... WELL THANKS GUYS, I FEEL TRICKED INTO TYPING BOGUS.