There's a lot more to the frequency response of a loudspeaker than the on axis anechoic measurement. The proof this that a lot of speakers which measure flat don't sound flat and don't even sound like each other. Total power radiated, room acoustics, and speaker placement are big factors in how a speaker will sound in a given system. Equalization gives you at least one powerful means to adapt the system to the environment. Without it, you hook it up, turn it on, and that's it, good bad or otherwise.

As for having a different equalizer for each input, I think that's a great idea and have toyed with it myself for a while. The ability to null out any minor spectral deviations from neutrality from each component individually makes a lot of sense considering how little equalizers cost today. An alternative is a digital equalizer with a series of memories, one for each input.