Troll Bra? Srsly? Most other names are okay to good, but Troll Bra? What were you thinking?
Otherwise I'm not sure all the ideas make sense.
Goldbrickers are exclusive to CaD, proper Clockwork actually only exist in Paragon City. Tons of Spoilers here, but there's a reason only CoH Clockwork appear to be building new ones.
Sure, there's Skulls in Mercy, so a Snake should be able to score some Dyne. But I don't know, it doesn't sit well with me. The Snakes claim to be high and mighty survivors of some ancient civilization. Shooting up junk would seem anathema to that stance.
There are Fire Thorn Casters and Behemoths with Fire Powers already, and Bat'Zul type enemies really don't play a large role in the game. Plain don't see the need for the Heretic.
Fire Maven? Biggest problem here is that the Cabal is all female while the Hellions are all male. Classical setups really. Feminist neopagans vs. macho street gang. They're literally fire and water. Can't see how they'd mix.
Trying to figure out how a Magmite/DE chimera would come to be. They'd essentially need to devour it first. Which would, well, turn it into a Devoured. Bedrocks are literally animated rock for all I know.
Vaz Abominations and Eidolons are already made from the parts of Superheroes if you read their fluff text. I wouldn't know where something made from bad quality Troll parts would fall in on that scale.
Tarantula Tanker? Uh. Despite the name I imagine a Freak Tank with a Fortunata welded to his back. No idea why. Seems technically doable. Not sure if they wouldn't need to code a new skeleton for this though. Which would kind of ruin the idea.
Magic is Magic. I don't really think you'd need an explanation for Midnight Squad 'wizards' to develop different powers. And the Winter Horde really doesn't need new enemies. Plus, since everyone gets to fight the WH it'd be silly if Heroes spawned Midnight Squad enemies to fight.
"If you're going through hell, keep going."
Winston Churchill
Winston Churchill
There is a very valid reason why new members are needed for all these groups. Repeated missions of these groups makes people bored because the gameplay is always the same. I have done the Positron TF at least 16 times between my accounts. Everybody starts falling asleep or losing interest half way through. Clocks mobs are always the same and every Clock mob boss is identical. Fighting mob bosses are the same as fighting the mission end bosses. There are far too many undeveloped groups of NPCs who have a small core of developed characters and then have been the same ever since. Something as small as adding new different bosses for let say 10 groups helps a lot. If I was NC I would have a critter creator contest to have people design new bosses for some of the neglected groups. Those new bosses put a lot of replay value into existing missions., into radio missions and any long set of missions using the same group.
I can go into the MA and create 5 mission with the Tsoo and each of those missions will be a very different play experience. That is what helps keep people interested and playing. Otherwise COH is going done the same path that D&D did way back in the start days. Orc Orc Orcs BORED with Orcs Wizard Wizard hires Orcs.
Adding new foes is a good idea.
Some of particular ones you've given us have problems though, as the poster above has mentioned.
Warriors with Rikti Swords? Sounds good, but I always imagined the Warriors' love of melee weapons to be a love of the more classic european midieval weapons, which Rikti tools are not. That being said, I'm rather surprised that they haven't taken up Shields yet.
The Freakshow would be willing to take up new and unusual weapons. Ever fight Sneaky Freaks or Noise Tanks? 
There's one Freak ingame who openly talks of his desire to weld himself to a sportscar and become a centaur. No, a Car-taur!.
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Adding new foes is a good idea.
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Nobody's arguing that point. More diversity is always more fun. It's just the particular implementation the OP lays out that I don't like. Mostly because a lot of his ideas don't make a lot of sense considering the background of CoX.
Also, some groups like Minions of Igneous and Bat'zul simply play a very small part in the game as it is. To put them in need of more diversity, you'd have to add more content featuring them, really.
"If you're going through hell, keep going."
Winston Churchill
Winston Churchill
I think that there are players who could go for groups like the Warriors to be expanded, both in depth of the faction's cast and thier role in the storyline.
Igneous? Probably not so much.
If I were a Dev, (and I'm NOT) I would look at the Player's use of existing factions in the AE, and ask the forumites directly which factions they like to fight and which ones could use a little more fleshing out.
Then I'd take the results with a huge grain of salt.
Is there a reason CoV enemies never were ported over to CoH? Like the various CoT enemies (hordlings, succubi). Is it a lore thing? Is it something that would take a significant time investment? I have never understood.
Sermon
@sermon
One of Six, Cannibal 6
This thread is to post suggestions for NPC Bosses which can be used by more than one group. This would promote more variety in the groups where there is only one boss type so all the missions play out the same. It would also get two groups more variety for one new NPC so its a two-fer.
Golden Clockwork (Goldbrickers and Clockwork) This is a Clockwork which has been built out of scavenged Goldbricker armor. It would be like a Cannon Boss but with Sonic Powers.
Troll-bra or Supa Cobra (Snakes and Trolls) . This is a Snake which has augmented its powers by taking Superadine. It would be a brutal combination of strength and quickness.
Heretic of Batzul (Circle of Thorns, Batzul) . This would be a COT Boss mage with Flame Powers instead of holds. These are the COT Mages who bargain with Batzul for increased power.
Fire Maven (Cabal & Hellion) The Cabal would recruit powerful Hellions with their arcane fire knowledge and teach them their knowledge of storms. It would be somewhere between a storm defender and a Damned.
Magmite Bedrock (Devouring Earth & Igneous) - A strange creature of rock which hears the call of the Hamidon but also the strange force which drives the Igneous.
Rikti Sword Slasher - (Warriors & Rikti) . Warriors who live with the Rikti to learn how to use the powerful Rikti Sword. Its the worst possible case , the skill with swords of a Warrior and the Rikti Sword technology
Supa Cadaver - (Vahilzok & Trolls) Vahilzok Zombies created from Troll parts.
Tarantula Tanker (Freakshow , Arachnos). I am not so sure this is a good idea. Its a Freakshow Tanker who has upgraded themselves by welding to a Tarantula Mistress rig from Arachnos.
Blight Apprentice (Midnight Squad & Winter Horde) - This would be a group of arcane students from the Midnight Squad who study the powers of the Winter Horde. So Force powers of the midnighters combined with cold domination or cold melee.