Depends. They have weapons with slightly alternate effects, like different shooters/rollers, or they could be like Mega Man/Palutena and have completely unique customs, spanning all 3 basic weapon types and a bunch of different sub-weapons (grenades/bombs).
As for their special weapons, it's hard to peg down just one, which is why I suggested something like Ryu's alternate Final Smashes would be great. The 3 "iconic" special weapons that come to mind are Inkzooka (bazooka), Inkstrike (tornado/nuke) and Kraken (Giant Squid), with a few others like Killer Wail (giant laser/SONIC BOOM) and Bubblers (invincible shield) also making sense. I can't for the life of me think of any way they could be "balanced" to just being customs. Maybe if they had really long charge times, or something similar to Mac's K.O. meter?
Thinking of how anyone could come up with anything with so many possibilities... but then I think of how perfectly Mega Man was done.