A: Secondaries that shoot more than one type of projectile. Like one point would shoot one rocket while the other would shoot another type when you click secondary fire.
You could check for keypresses and mouse presses with scripting and create a weapon with the appropriate speed, position, orientation, and target (though you might have to manually set up gunpoint data for each ship). This wouldn't work for the AI (it has no intelligence for this sort of thing and doesn't work via the keyboard/mouse input code), and it wouldn't work if the player remapped the keyboard or mouse or used a joystick.
B: Barrage fire. Where pressing the secondary button results in several seconds of firing rather than having to hold it down.
I've seen this done, in Blaise Russel's FS1-era FS2Open campaigns, if I remember right. I think it's done by $Swarm.
C: Animation. Seriously I know there are techincally incredibly limited and rubby animation commands that let you rotate a subobject, but I want to know if it is AT ALL possible to add in even an animated model. Like you go left, change character animation to animation_6 or something. Even just armoured core level of animation would be acceptable.
You can rotate subobjects, but that's about it. Anything else requires writing your own animation system using multiple models (which for this purpose would be analogous with 'ships'. You'd need a ship class for each arm, leg, etc. or do something bizarre like having the complete model, destroying all the subobjects but the limb you were going to use, and then using multiple ships of that type with different positions to create the full model. So you'd have a 'mecha' model, then you'd kill every subobject but the head subobject, move that vertically. Then you'd make another 'mecha' ship, kill everything but the right leg subobject, and move that down and to the right, etc. All that would be part of your render function, which would handle changing each ship's orientation/position to animate each ship. You'd also have to account for the ships hitting each other - that would be bad.)
D: Notices when another player fires a specific weapon. Like when they fire it a comms message triggers. I'm actually fairly sure this could be done with SEXPS.
You could use scripting to go through all the weapon objects and compare the parent to the current player. If the weapon is newer than the last check, you set a SEXP variable. Then you set up a SEXP conditional to check if that variable has been set via scripting, unset it, and send the message.
You might be right about it being doable with pure SEXPs, but that's how you could do it with scripting. I don't know about pure SEXPs.
EDIT: Conceptual corrections, the engine should handle drawing ships for the mecha thing, you should just have to move them in order to get the animation effect you want. Note that some kind of fluid half-life 2 animation thing is going to require a lot more work and probably can't be done without lowlevel engine modifications, new vertex shaders, etc.