A) Do you feel confused seeing more than one person with similar names? (e.g. Squall, Squall82, SquallFFVIII, Squall4ever; Zell, Zell 007, Zell69)

This doesn't really confuse me. Unless people start calling other members by letter(example: Sita Atis = SA or rikkuyuna89= RY)

B) How would you feel if someone registered with a similar name as your own? (e.g. as of now Agent Proto is the only known Proto, but someone registers as Proto Man and likes to be called by Proto)

I dunno exactly. That never really happened to me... how do you make a new name out of "Triple T" anyway?