Well since you've been more than frank, I'm going to go ahead and do the same:

I don't understand the exclusion of crouching and melee, along with the lack of the morph ball it actually feels like movement has been dumbed down quite a bit.

Yeah, it has dumbed down a bit because you aren't stuck on one tier of the multi-tiered terrain, rolling around in a lethargic ball, dropping bombs. You don't need crouching, you halotard Melee might be added, but we'll see.

For some reason, practically everything has homing. There's no reason for that, only missiles and the wave beam charge shot should have homing.

Sorry, go play Metroid Prime. Every charged beam, and actually every beam has homing when locked. Since we can't have locking without the use of an app, that's what you get.

The lack of any sort of pickups makes the environment completely pointless to explore, and starting with all the weapons means you can basically just figure out which beam you prefer and never change from it. It would be better if the weapons were all pickups, and they could even be colored spheres like in Hunters for more metroidy flavor. Some other items from the Metroid universe would be nice as well, such as perhaps a phazon beam for uber spraying and a sonic boom that sends people flying

You are right, there is a lack of pickups and environment exploration, because we released two small-sized maps. Deal with it. There's a constant barrage of health and missiles to pick up. The weapons aren't going to be little orbs for you to pick up, it's bad enough arranging everything in the first place, let alone making you dash over to some area to get your favorite beam. And, you've obviously not had any interaction with the Halo Editing Kit in awhile, or you'd know why we only had the number of beams we did and why we dropped one for oddball and ctf: you can only hold 4 weapons/items at a time.

Power beam stuns enemies, charge shot gets headshots

No it won't, do you have ANY idea how annoying stun is in Halo online? You try getting one person to play the mod after that addition, I doubt it would happen. Charge shot shouldn't have headshots, if anything should it should be the only beam somewhat like a sniper rifle, the Plasma beam.

Plasma beam has a scope, charge shot sets fires that do actual damage

Scope is an ok idea, but once you zoom in, we'd have to create a faux HUD on the scope itself, or make a weird-looking custom one. Fire is about as annoying as stun. You just dance around, on fire, and you really can't judge when you are about to keel over and die, SORTA LIKE THE FLAMETHROWER!

Wave beam annoys people with purple screen flashes, charge shot has homing and a more intense screen flash

We.. have that already?

Havoc beam and missiles are pretty much fine as they are, though the missile damage could use some rebalancing.

We made the missile damage the way it is to balance out the beams. If you aren't precise with your plasma fire (any of the beams), we give you a missile, similar to a grenade in damage and shockwave (manner that it pushes you backwards/propels you). It's a glorified grenade, trust me.

The Power Beam effects are pretty schizophrenic, they should all be yellow not rainbow colored

They are yellow with a slight blue contrail encasing them.

The wave beam charge trail doesn't always line up straight (though the rest of the wave beam effects are fantastic)

That's because of homing then, or the way Halo handles contrails, not really that big of a deal if you can deal with something not being perfect that you can't change.

The arm cannon still isn't shiny, and the arm cannon permutations should be a little more pronounced. At times it was hard to tell what beam I was even using

The shininess is something we could fix easily, I'll look into that. The arm cannon permutations are also marked by a specific display on the bottom right to show you what beam you are using. The box slides into the middle, the colors represent each beam: power, havoc, wave, and plasma. Shoot one, you should be able to figure out which one is which.

The Plasma Pistol reticle needs to go, the R aiming reticle from Prime would be better

I agree, but it sorta gets in the way, we chose a minimalistic reticle for the mod, so there wasn't a huge scope the size of 4 people's heads in the middle of your HUD.

There's no need to have the arm cannon come back up when picking up the flag, since all the beams have the arm cannon in the same place, just have the animation for taking out the flag have samus move the arm cannon over a bit

There sorta is a reason, it's used for melee. It actually (if you look at it) pulls up, out of the way. It's not like you can't see with it there, we just made it that way to show that you still had the ability to use your cannon.

The dying animation is pretty lame, a nice explosion would be better. With no damage, but a bit of force maybe (especially since the animation plays an explosion sound)

A 'nice explosion' causes exceptions. You have problems when you make the biped disappear, trust me, a LOT of problems. The animation plays a death sound and the sound of her suit shutting down, I don't recall an explosion..

The charge beam balls are way off in third person, and don't seem to give off any light

They give off light, go into 3rd person in a LAN server, and you'll see. We know about the charge balls, we'd just have to move them by hand, and we didn't have the opportunity, since we were working on more important things.