When you really think about it, MGS characters would be on the same boat if there were also 7 of them in Smash, as most of them indeed look similar (not Raiden, for sure), specially for those not into the games. Such is what happens when more realistic-looking characters are put amongst cartoony characters with more obvious, distinguishable features. It does not help that 5 out of 7 from them also play very similar as well.

I think that if the characters from both MGS and Fire Emblem were chosen with move diversity in mind, they might be more distinguishable from each other.
Someone like Col. Volgin, who is pretty much melee only and has lightning powers, could stand out in the same way that a Fire Emblem character with a lance, axe or hammer could stand out from the other Fire Emblem characters who only use swords.