Dude this is a really awesome character sheet. I love the logbook pictures scattered around. This is prime shit my dude.
As for progression, a good way to introduce other types of Pirates would be to either make a small squad of something like 2 or 3 Aerotroopers or sprinkle one into a group of normal Pirates to make them stand out more. The second method could even make them like small mini-bosses, which would really make an impact when the players start seeing them as normal enemies.
If you really want to make your players shit themselves, try the dual Grenchler fight in some varying degrees of water. Their invulnerable hide makes players really freak out and it's always hilarious to watch without it being some immortal death beast. The Space Pirate Hussar in a cramped room or 2-3 Aerotroopers ambushing players on a crumbling cliff side is also pretty challenging.
An encounter I always wanted to try was an exotic lifeform containment unit of sorts with heavily secured doors. Going further and further into the facility requires a Ops Trooper to disable levels of security similar to Metroid Fusion, with a few small areas opening up with nothing really in them. Upon disabling the final layer of security to get to their objective, the containment units open up, letting out a bunch of creatures and a small pack of Metroid the players have to dodge or subdue as they try to escape the hellhole they just created. Add optional functionality in the individual containment pods so players can attempt to trap more dangerous lifeforms instead of just gunning them down.
Or you could do some Resident Evil 3 "Nemesis is hunting you" shenanigans with some Chozo Ruins and a Chozo Ghost phasing in and out occasionally. Really fun if your players are easily spooked. In general, I find making the environment more important that the mobs but you can't really disregard them entirely.
Sorry for the rambling, I just like that people are playing my game.