An interesting question. I know at least three different things use AEGIS as its SHIELD stand in (Masks even references them in their copyright spiel at the beginning of the book) so I feel like that is something that can be gotten away with.
That said, one of my friends from the Sentinels card game offered up his SHIELD stand-in–The Division–to replace AEGIS if we wanted it. Their version is an FBI off-shot that grew beyond its original purpose and have several different sub-division. For instance, Division 2 was originally in charge of Nation Affairs, but over time has shifted to handling superhuman relations.
Their character, Tucker (from this deck) is a member of Division 6, which handles Supernatural Affairs, and is a bit like a combination of the X-Files and the BRPD. Anything that isn’t Division 6 hasn’t been too fleshed out beyond a high level.
All that said, I am more interested in whatever everyone else thinks (in particular Bill and Dave since this change more greatly affect their characters). Keep it AEGIS, go with the Division, or come up with something original?