Okay. You're in command of SHIELD, an intelligence agency dedicated to protecting humanity and the world. You've been made aware of threats by forces known, unknown, shadowy, and superhuman, intent on engaging in a "higher form of war." Thanks to a synchronicity of special individuals, events, and artifacts, you were able to help win the first spectacular engagement in such a war. Unfortunately, along the way, your secret, plan A, defense was revealed to be built on tech developed by or co-opted from the Bad Guys of earlier conflicts. When this is uncovered, the Good Guys (many of whom might individually be considered WMDs) take issue, apparently on moral grounds. So, the tech is destroyed, or at best, mothballed.
But how can you count on being AVENGERS-lucky in a consistent way when new, supernatural threats from unexpected quarters arise with greater and greater frequency? You can't.
We know that Fury wants Earth, humanity, but most especially, SHIELD to be ready, properly armed, to combat the powerful and dangerous forces involved when fighting a "higher form of war." But, he knows that the greatest advancements in tech and enhancement require taking steps that most men and women who believe themselves to be good, moral people, would not agree to. At least not in the light of day. So, how to take those steps without actually taking them?
Have the people who don't care about being seen taking those steps take them. The scientists and businessmen and despots and just plain villains who don't care about being branded "Bad Guys," or who consider themselves and their work beyond such a naive concept, they can develop and test the next generation of WMDs in the wild, unregulated, without oversight. SHIELD identifies and brands them as the enemy, a threat to security, the common good, even existence, then captures them and appropriates their advanced tech, weapons, and research.
Yes, such progress is made at the cost of others' well-being and safety, perhaps involving extortion, blackmail, mind control, and murder, but it's made. By the Bad Guys. Not SHIELD. But hey! Why throw away a perfectly functional Chitauri blaster, right? Why not reproduce and perfect the dimensional portal opener that accidentally trapped an unwitting guinea pig between dimensions? Why not use the super soldier serum knock-off since it's been perfected (after hundreds of mortal failures)? Some of these Bad Guys might be self-made, but others could be run from a disavowed, invisible arm of SHIELD, some branch granted its own initiative—kind of like a dark version of Coulson's team—branch that might produce something like Centipede.
So all this rambling means is that I like Centipede as a a straw man and incubator for SHIELD R&D. I would *LOVE* for it to have been masterminded by a SHIELD Agent from the future (who in our present might come to be called the Clairvoyant, no?). An Agent who survived a reality without Centipede and the stronger SHIELD that it enables, a SHIELD that is/would've been properly armed to deal with a catastrophic threat that destroys the world, or America, at least. =)
Maybe the future Agent is Nick himself, or a apocalypse-hardened Coulson, or… a Deathlok. Would *love* to see present and/or future Deathlok side-by-side w Cap in an episode or movie! =)
Hrm… Does "WWFD?" work better than "WWNFD?"
In a completely unrelated bit of theory crazy talk…
I would love for the ultimate conflict w Thanos (most likely involving a certain set of reality-shaping stones) to be resolved in part by Captain America seizing the gauntlet/staff/raincoat/whatnot of Infinity and using it to reverse all of the terror, tragedies, and deaths caused by the machinations of the Mad Titan and the Elders of the Universe, but, with just a little something extra—a little reality tweak for Cap himself, an order to the stones to rewrite the universe so that he could be reunited with his best friend Bucky Barnes, thusly rewriting a timeline that we may never see into the one that we do see in WINTER SOLDIER. That would be crazy, tho, right?
Keep on keepin on~