Works well with the "agent level" theme I envision for this RP. I don't want the party so buff that I have to send a Chitauri invasion or an army of Ultrons to challenge them. Hydra, AIM, Extremis and Centipede enhanced and such are within SHIELD's ballpark, and AEGIS is just the next level above that, dealing with the threats that lie between SHIELD level and Avenger level. ( meaning most missions won't be so massive as to get world media coverage and won't quite be preventing extinction level events)
In other words, if I present the party with a trained team of Hydra agents led by an enhanced, they won't just assume victory is assured, and wonder when they can go after that alternate reality Doctor Doom wearing Vibranium armor.
I hope you get where I'm going with this.