With regards to Lil Dog's comment about brutes and drones, they didn't have their entire species on High Charity. Brutes occupy vast stretches of space just like many other species in the Covenant, and I'd say something similar with regards to drones, but I'm not actually certain. I'd love to set the game to easy and try to punch down hoards of brutes like in the good ol' days!
Most of those ideas are fantastic, and a few would be fairly easy to implement. Some of the new things, reptilian beast, mini-scarab, (The Locust's kinda like that) and since they aren't in the game, brutes and drones, would take a fair bit of effort to use. They've got a sorta-flood, but I'd like to see it more bloaty and infected again.
The Pelican mission is an amazing idea, especially since it's already designed for three people to be able to use it. And it's in the game already! Just stick a turret in the back or something for the fourth guy. Broadswords would be interesting until your teammate decides to knock you into a wall and send you both to fiery oblivion.
I like the alternate objectives as well, keeping Majestic alive instead of a bunch of scientists sounds much easier. The bomb arming would probably end up like the chapter where you disarm all the Havoks, except in reverse. With regards to the MAC, they could always bring back the Mammoth. It's got vehicles, turrets, the MAC, of course, and enough weapons to keep four people stocked for a whole chapter. Defense, assault, whatever. First person to the targeter gets to fire it!
The Flood missions are really easy as far as story goes, there are Flood on Halos, there are containment procedures, there are idiots to release Flood. It writes itself. Again, I'd like to see them bloatier and more infected.
As a final thought, I'd like to see some in-game mention of the Precursors. Nothing major, just tidbits. Maybe a mission where you find a not-quite Forerunner artifact or something.