I didn't really give much thought to the idea of them being attacked, but I'd say no. I'd think it much better if they were kinda almost "glued" to Paper Mario's side like how they follow you around in the games wherever you go. You jump, they jump. However this wouldn't be exactly glued but again more like in the games where they sort of run and jump after you. However if you were able to think up some good reasons why they should be attacked and thus separately KO'able (remember in PM1 you weren't able to attack partners as such to KO them!) then I'd still advocate that you'd be able to bring out another partner should you not also be KO'd.
Your favourite partners too? Great minds think alike I see! I wanted to include Watt as well but couldn't really see her moves fitting in at all. About Parakarry, I really couldn't imagine implementing his moves in either. Air Raid definitely for a Final Smash (if you've gotten that far in PM yet) but Shell Shot would require either homing mechanics (imbalanced) or would have to function in a set direction diagonally and thus you may as well replace with Kooper. Parakarry would be good in that you could replace the airplane with flying while he was out, but if you've got suggestions for implementations of Sky Dive and Air Lift then please say so ^^.
Agreed on paintbrush boy having a better chance unfortunately :/ But like you, I too would prefer to see Paper Mario appearing in Doc's shoes, especially with something like my moveset. Are 2 Mario representatives all that unlikely? If Pokemon is to get an estimated 6 and Mario has 5 but is losing 1 then I could stand to see Mario getting +2. With Toad almost all but out of the picture
it looks like the options of decent characters are running out. Am I the only one that thinks that the Master should be an option? He'd be able to have awesome moves :D.
By the way, if anyone has any moveset requests for decent characters I may or may not have a go at giving it a shot, subject to whether I've played his games or like the character. Thinking of maybe giving a ToS character a shot (who'd be another awesome, yet unlikely, character choice
).