I know I'm late to this, but all it depends on is what you want.

Both are very good units however Shisui [Susano'o] BTs is the best unit currently (until Guy [Gate of Death] picks up more steam). I prefer 6-Paths Pain because he's more fun for team building and Shisui IS a majority of team building which makes Shisui very stale to see and use after a while, but it's a matter of preference. Both are good choices. Go with your gut feeling.

Hey, no problem! I apologize that this response is so late, I'm currently on vacation but decided to check in on forums.

Pain-Tendo [Six Paths Rinnegan] is a weird unit. He gains more attacks from non-traditional debuffs, whereas most other standard attack units gain their attacks from statuses or kills, 6-Paths Pain can get a standard attack from any form of debuff. If you have a unit that applies a non-status related debuff on an opponent when hit (I.e. "Units attacking Shisui will have their Critical Rate reduced by 50% (not stackable) until the end of the round.") then 6-Paths Pain will nullify that reduction and, even if it's not stackable, continue to "receive" that reduction. At-least, that is my understanding of how he functions.

I have used him rather infrequently as my server avidly uses Shisui [Susano'o] 4* so I tend to use him as well to counter being KO'd round 1, so I don't have any clue if he actually does nullify these stat debuffs in any way, but I do seem to get critical hits with him as much as other units when fighting Shisui so... take what I said above about nullifying stat debuffs with a grain of salt. Standard attack units in general are weird, sometimes I have only applied 1 or 2 debuffs to Shisui and he will attack 5-6 times, someone more interested in these systems than myself will have to answer these oddities but this is my conjecture based on what I know.

Hope that helps!