To clarify, the Kages in question are Hashirama, Tobirama, Hiruzen, Minato, Tsunade, Kakashi, Naruto, The Third Raikage, Ay, Darui, Mu, Onoki, Kurotsuchi, Gengetsu, Yagura, Mei, Chōjurō, The Third Kazekage, Rasa and Gaara.
Pein defeats without much trouble the following: Kakashi, Hiruzen, Rasa, The Third Kazekage, Mei, Chojuro, Darui, Tsunade.
Pein likely defeats the following with medium difficulties or something close to it: Mu, Onoki, Gengetsu, Third Raikage.
Mu and Oonoki can only depend on Jinton for victory, but both lack the means to actually get it off on Pein. Mu can avoid being thrust down onto a chakra spike by turning invisible, but that only prompts Pein to use his rain sensing technique and then unleashing Asura's missles to pepper him out. Oonoki's best bet is to use clones and doton to distract Pein, but with shared vision and how unimpressive the doton clones are, I don't see how he lasts too long.
Gengetsu is soundly defeated with Asura or Deva clearing the field of mist and then targetting the clam. Joki Boi can be repelled somewhat easily, shinra tensei or the Preta Path defends the group largely. The Mizukage gets his soul taken, in the end. I really only see The Third Raikage being defeated the same way. None of Pein's moves, apart from possibly a larger Shinra Tensei, should do bodily harm to the Raikage. I don't think the Raikage's quick enough to blitz Pein, at least not from this distance. Using the Asura path to restrain The Raikage and trying to take his soul as quickly as possible is really the only option I see available. Possibly a large enough Shinra Tensei, but I'm not sure on that.
Pein either beats or loses to these kages with a display of greater effort: Tobirama, Gaara, Ay, Minato
I'm not sure how Pein would be able to react to FTG. On one hand, from this distance I don't see Pein making the mistake of allowing too many Kunai marked enter his space. But if either does manage to weave in and around the Paths, I don't see anything short of a large scale Shinra Tensei clearing the area of the Kunai. A five second interval isn't short for Tobirama or Minato, at least not with their striking speed and how quickly either can close a gap. Add in shadow clones, and I don't see Pein normally clearing it.
Ay, I'm not too sure how Pein deals with his speed once he gets into close range. V2 should be murder on him, but if he can defeat him in the same method as his father or somehow prevent him from getting too close, I'd give Pein the win. Otherwise I see Paths being taken out with extreme hostility before it comes down to Deva and Ay. Chibaku Tensei's probably the likeliest way he'd win.
Gaara I am mixed on, because I'm not sure how well Pein would do with losing the environment control. With the entire region as a desert, Gaara could literally drag some paths down a few feet and squeeze the life out of them or damage them greatly. It shouldn't take more then a few minutes for Gaara to teraform the entire region, either. With full intel, I see Gaara being able to aim and dismantle the Naraka Path. His defense is good, too. With being able to block Pein's LoS and with sand capable of outlasting missiles or the summonings, I don't really see Pein being able to conventionally defeat Gaara unless he resorts to Chibaku Tensei.