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Since even with custom names/descriptions I've already seen they'll get me complaints of "Why is there Council/5th Column here?"
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People will complain no matter what you do. Create your arc the way you want it and however it makes you happy. Don't pay too much attention to what everyone else thinks. You'll never satisfy everyone. 
Shard Warrior - 50 MA/Regen/BM Scrapper
Founding Member and Leader : Shadow-Force
Co-Leader: Council of Heroes
"Whatever evils come this way... we will be there to stop them."
For level 40+ you could use Council Empire, they look more like generic military guys and less like Council. The Crey swat dudes might work for the 30s, as might some of the 20-35 PPD. You might even be able to get away with some of the gun-toting Longbow, depending on what you do with the costumes.
Eva Destruction AR/Fire/Munitions Blaster
Darkfire Avenger DM/SD/Body Scrapper
Arc ID#161629 Freaks, Geeks, and Men in Black
Arc ID#431270 Until the End of the World
Sounds like what you're looking for are the Spetsnaz Commandos. Unfortunately, they're too low for the level range you intend to use here. Next-best group for generic military I'd say are Sky Raiders. They have no logos, and if you just grab the jetpack-less ones and fiddle with the colors some, you can easily pass them off as an entirely different group.
"If I had Force powers, vacuum or not my cape/clothes/hair would always be blowing in the Dramatic Wind." - Tenzhi
Characters
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Since even with custom names/descriptions I've already seen they'll get me complaints of "Why is there Council/5th Column here?"
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People will complain no matter what you do. Create your arc the way you want it and however it makes you happy. Don't pay too much attention to what everyone else thinks. You'll never satisfy everyone.
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I understand that much, but if it's a complaint that I can address. Why not do so?
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For level 40+ you could use Council Empire, they look more like generic military guys and less like Council.
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That idea I already had, since they look like Malta with Council Masks.
I'm working on a villain group that several of my story arcs will focus around. They're kind of a homage to groups like Cobra, Hydra, Kobra, AIM, and Big Fire. Their intended level range is 25-54.
I want them to have the mixed military feel you get with groups like the 5th Column and Council. So at the moment I'm mainly using customized versions of the Council's 25-54 troops and a few of the Malta guys at the higher levels. There are some monsters and a few custom enemies mixed into the group for various reasons. But I'm wondering if anyone has any suggestions for something that has less of a uniform look then Council or 5th Column. Since even with custom names/descriptions I've already seen they'll get me complaints of "Why is there Council/5th Column here?"