3. It Screws Up S.H.I.E.L.D.
In Civil War, the "Strategic Hazard Intervention Espionage Logistics Directorate" are a group of order-following, hero capturing bureaucrats who, with Iron Man, lead the charge for superhuman registration and interment. They are led by Director Maria Hill, who is an utterly unlikable, ambition-focused, back-stabby kind of girl. S.H.I.E.L.D's role in the Civil War very much paints them as the evil empire, rounding up well-loved superheroes and imprisoning them without due process in a super prison within the Negative Zone. In the MCU, the "Strategic Homeland Intervention, Enforcement and Logistics Division" are more like the government black sheep who the suits wish they didn't need, but do. They are led by Nick Fury, a no-nonsense boss who has no problem making tough choices, but always follows his unflappable moral compass (even when it's unpopular with the powers that be). Fury is joined by a loyal and likable Maria Hill (played by the always likable Cobie Smulders) and super loyal and likable Agent Phil Coulson (played by renown jokester Clark Gregg). S.H.I.E.L.D's involvement in the Civil War is too big to ignore or convincingly change. It would require firing Nick Fury, changing everything that works about Maria Hill as a character, and completely changing the already established relationships that Iron Man and Captain America have with S.H.I.E.L.D. Not to mention, Marvel just put out the "Agents of S.H.I.E.L.D" tv show, reanimating dear Agent Coulson to take the lead. As far as the film/tv S.H.I.E.L.D goes, it ain't broke, so Marvel ain't gonna try fixing it.