Wow, beating Charlotte with that team, even with Rain Dance is quite a feat. I'm not saying it's bad, it's just not all that great.
Now, that's a really odd Swampy set. I'd recommend Earthquake to stay, but everything else could go. Go back to the circus and get yourself the Dive HM (required for the next episode anyways). Muddy Water has terrible accuracy and Surf is coming off of the weaker Sp.Attack stat as well as Muddy Water, so Dive would be better than those two. Then there's Hammer Arm, a good move on Swampert considering it won't outspeed too many foes anyways. Endeavor can be situationally useful as well. Another thing worth getting from the Circus would be the Tirtouga from one of the slidey image puzzles (solutions can be found in the game's folder>Graphics>Pictures>Tile Puzzles). That Tirtouga can be used to get breed Rock Slide onto Swampert.
Honestly, there's far better stuff out there than Golem. Sure, it's attack and phys defense are nice, but that's it. Low Speed, no special defense whatsoever, many and common weaknesses and not exactly the most attractive moveset.
If you want to keep it, you should maybe get rid of Rock Blast, it only has a 16.7% chance of hitting 5 times, in all other cases it's equal to or weaker than Stone Edge. Due to STAB, Earthquake and Stone Edge have 150 Base Power, while Explosion has 250, I'd recommend something like Heavy Slam over Explosion.
Dark Pulse and Shadowball have the same Super-effective coverage, but Dark Pulse gets STAB, so instead of Shadow Ball, you could breed Sludge Bomb (via Smeargle is the fastest/easiest way) or maybe use that Hidden Power TM (HP Grass would be sweet).
Final Gambit oughta be broken still (i think). Anyways, Sleep was nerfed to last only 1-3 turns, so rather than Yawn, you could use Giga Drain. Acid Spray is also an amazing move (for support at least). Body Slam and it's 30% paralysis chance are also neat. U-Turn is really more of a competitive move, not all tha useful in-game. Although Accelgor really isn't that good. Excellent speed, good Special Attack but not enough to one-shot foes thus preventing getting one-shotted yourself, no defenses. I'd recommend switching it.
Well, yeah, Moonblast>Teleport, but not much else to say. You could get Thunderbolt via Stunfisk.
There's better. Especially if you use a set like that.
Since you said you want suggestions and you have rotation team members, I'll just copy-paste a complete list of stuff I consider to be very useful in Reborn (i do a lot of these team showcase threads):
Nidoking (Ice Beam and Thunderbolt via Smeargle, Flamethrower via TM)
Arcanine (Close Combat via Primeape/Zangoose)
Gengar (Sludge Bomb and Thunderbolt via Stunfisk>Grimer>Gengar)
Kingdra (Dragon Scales are randomly found on Horsea) (Ice Beam via Remoraid)
Crobat (Physical with Zen Headbutt via Hoothoot or U-Turn via Archeops; or Special with Nasty Plot via Honchkrow)
Ampharos (Agility via Growlithe/Buneary/Buizel/ a lot more)
Azumarill (Belly Drum via Poliwag and Aqua Jet via Golduck/Seel/Tirtouga/Buizel)
Heracross (Earhtquake and Rock Slide via Geodude>Crustle>Heracross)
Sharpedo with Speed Boost (Waterfall and Destiny Bond via Goldeen>Qwilfish>Carvanha)(Protect, Waterfall and Destiny Bond via Tirtouga>Remoraid>Goldeen>Qwilfish>Carvanha)
Walrein (Signal Beam via Mareep/Remoraid/Seel)
Empoleon (Ice Beam, Scald and Agility via Smeargle)
Staraptor (U-Turn via Archeops)
Roserade (with Technician for a 90 BP Hidden Power) (Sludge Bomb via Muk>Stunfisk>Wooper>Snubbull>Roselia (not Budew))
Mismagius (Thunderbolt and Psychic via Stunfisk>Ralts>Misdreavus)
Bronzong
Drapion (Swords Dance and X-Scissor via Ninjask)
Magnezone
Yanmega (Psychic via Venomoth)
Mamoswine (Rock Tomb via Smeargle, Rock Slide via Camerupt/Drilbur/Smeargle)
Gallade
Froslass
Excadrill (Poison Jab and X-Scissor via Smeargle)
Leavanny (Sticky Web is learned at level 31 by Sewaddle and not by Swadloon/Leavanny)
Darmanitan (Rock Slide via Camerupt/Drilbur/Smeargle, Dig via Diglett/Smeargle)
Krookodile (Stone Edge via Rhyhorn/Smeargle, Rock Tomb via Smeargle, Rock Slide via Camerupt/Drilbur/Smeargle)
Scolipede (Poison Jab and Protect via Pineco/Dustox/Burmy/Swadloon>Beedrill/Ariados>Venipede)
Scrafty (Elemental Punches via Hitmonchan>Buneary>Scraggy, Dragon Dance via Altaria/Horsea)
Acrheops (Earthquake via Wooper>Corsola>Archen)
Cofagrigus (Psychic via Ralts, Nasty Plot and Memento via Spiritomb)
Escavalier (Knock Off via Skorupi)
Solosis
Gothitelle (Energy Ball and Dark Pulse via Petilil/Lotad>Cacturne>Gothita)
Galvantula (Energy Ball via Petilil/Lotad>Paras>Joltik)
Chandelure (Energy Ball and Flamethrower via Growlithe/Vulpix>Snubbull>Swirlix>Castform>Litwick)
Stunfisk (Earth Power via Corsola, Sludge Bomb via Grimer or Scald via Panpour>Psyduck/Wooper/Piplup/Buizel>Stunfisk)
Bouffalant (Earhtquake, Rock moves, Poison Jab, Wild Charge via Smeargle)
Bisharp (Sucker Punch via Cacturne/Spinda/Toxicroak, Psycho Cut via Alakazam)
Durant (Rock Slide via Dwebble)
Braviary
Bulky Chesnaught (Leech Seed, Spiky Shield, Synthesis (Gogoat/Seedot), Body Slam)
Gogoat
Heliolisk
Sylveon (Wish via Slurpuff>Pikachu/Skitty>Eevee)
Trevenant
Phantump
EDIT: Oh, by the way passing on TMs no longer works since E12, so you'd have to go back to that. Should you need any breeding help, feel free to PM me.