Well, personally I'd just be happy if they animated the Jinchuu arc. I really had no problems with the way the 1st season as well as the Kyoto arc played out in the anime. I never cared for any of the fillers that took place after the Kyoto arc (which basically make up ALL of the 3rd season ), but I found the anime to have done an excellent job of adapting the manga's story line up until Kenshin and frienRAB left from a successful mission in Kyoto to return back to Tokyo.
Honestly, the only reason that I couldn't call RK one of the best anime ever was simply because the anime itself lacked the best story arc in the series (and also had a ton of boring filler ). If I were to just see a new season of it covering the Jinchuu arc, though, that would be more than good enough for me, because I actually wouldn't want the anime to change anything it did up until the end of the Kyoto arc. I even actually liked and enjoyed most of the fillers in the 1st season, so aside from maybe digitally remastering the entire series like what Toei did for DBZ, I would rather just see the conclusion to the series in another season, rather than having the entire series needlessly remade.