Armor abilities fill a pretty awesome role in tying in gameplay to the lore of the universe. Since the Fall of Reach, we've known that Spartans have access to all manner of specialized equipment like thermal vision, thruster packs, multiple ammunition types, and different weapon components. Armor abilities are a window into that world of mission-specific gear.

Standard power-ups can stay the hell out, as far as I'm concerned. It never made sense to me that there were these magic boxes full of shield or invisibility just chillin' out in the world. Armor ability placement has a similar problem but at least the equipment makes some degree of sense. I wouldn't mind if the abilities were each a bigger deal; like a jetpack might be a miniature vehicle which allows regular movement and weapons fire, but also grants vertical mobility, instead of just being high-jump boots. Other abilities might be integrated into standard Mjolnir systems; we know the Elites pretty much all have access to recharging cloak technology, and the UNSC's been on that for years with the SPI's camo. To draw a gameplay analogy, in the Mass Effect multiplayer, Bioware started adding playable species with special abilities that weren't attached to the power wheel or hotbar: the Volus, instead of having a melee attack, had a simplified version of the tactical cloak and a shield regenerator. You couldn't level them up or augment them in the same way as normal abilities but they were still functional. If Master Chief could cloak for a few seconds or focus his shield into his gauntlet, I'd be happy.