Grand Patriarch: Prophet of Mercy:
The Prophet of Mercy is similar to other covanant, his only changes are the leader and super unit.
The Prophet of Mercy starts out exacly like regret, with shields and duel plasma cannons, however his upgrades and ability are vastly diffrent. The only Major change to the phrophet in the begginging is the speed, his is slightly faster.
Upgrade names are debatable, i didnt come up with anything like divine absolution, or perversion.
Upgrade 1: Heated Plasma
His Plasma Cannons do not change to Feulrods, however they do MUCH more damage (equivilant to fuelrods over time) and glow a slighly brighter blue(similar to how other units change to show an upgrade).
Upgrade 2:Advanced Shielding
Its what it sounds like, his shields go up. I would say by about 50%, thats a balancing issue though.
Upgrade 3:Combat Veterancy
The Prophet has seen to many wars.... with this upgrade, his is faster, does more damage, and is stronger (10% each ???). generaly stronger.
Now for the super ability.
The Prophet of Mercy is interesting, he has a type of plasma rifle like weapon. The ability brings you to a screen similar to cutter, but there is no bar to show were it hits next, the weapon itself is a plasma weapon from a ship above, and unlike the beams, it fires shots at the ground, this DOES NOT have 100% accurasy, but the shots do tremendoes damage to what they hit, and some small area of effect damage. It is like firing a plasma cannon from the sky, and there is a slight lag before it his (2 secondes?).
UPGRADE 1: The Weapon Shoots faster, so instead of shooting 1 shot per seconde, it shoots 2 (cost is based per seconde, so this is basicaly double damage.
UPGRADE 2: The Weapon Does Splash damage, this is similar to area of effect damage, except instead of just hiting you because your in the area of effect, units have a chance (small) of dodging it, like if you droped water on the floor, it splashes and droplets go everywere, but you might not get hit, depends on your size.
Upgrade 3: The Weapon could hit air units before, but with upgrade 3, it doesnt explode on the ground, it explodes above it, causing it to hit air units alot easyer, and to have way more splash damage, however, most of it still hits the target(damage from main shot changes from something similar to the mac, to more of a grenade in mid air, the explosion his alot more, but does less damage to the initial target, however, with the plasma, most of it still hits the target, so the damage does not change, the spead just gets bigger, and the air units are MUCH more vulnerable, like fuelrods at long distance, or from aa wratihs).
There's a lot of excellent stuff in this thread, but I feel compelled to comment on this one.
This is just wrong on so many levels. Prophets are political/religious leaders. They are not generals and they are definately not fighters. Fighting is beneath them. They have all the other Covenant races for that. Yes, their chairs may be armed, but they are not meant for battle. An army that is led by a Prophet is doomed. They know as much about battlefield tactics as a Brute Cheiftan knows about diplomacy.
Using the Prophet of Regret as a battlefield leader in Halo Wars was a mistake. If we're going to talk about a remake or Halo Wars2 the first thing that needs to happen is to agree whether or not to stick to basic canon or just throw it out the window. If you're going to stick with canon then your Covenant military leaders have to be Elites, Brutes, and possibly Jackals. Any of these races can rise to the level of Shipmaster and command troops. Replace the Prophet with someone cool like the Shipmaster from Halo2.
Other than that, everything else just might work.