Thanks for the help. I'm already up to the last 2 gyms now, so I dunno if I'll restart, but I'll try it to find out if that's what was wrong. I've been using YAPE to hack the pokemon movesets of the pokemon in my team so they learn the TMs I'd teach them naturally.. XD
Anyway, I wouldn't recommend giving a Feraligator that move set, honestly. Feraligator's a water pokemon. If you just give it moves you'd teach a Tyranitar or something, you might as well have a Tyranitar, considering it has a much higher Attack rating. Also, Feraligator doesn't have the Special Defense or Speed to take advantage of Sword Dance (or at least a type combo that gives a lot of resistances). I'd recommend something more like this for Feraligator:
Surf
Ice Beam
Earthquake
Brick Break
That gives it an offensive edge on Normal, Fire, Electrifc, Grass, Ice, Poison, Ground, Flying, Rock, Dragon, Dark, and Steel. If you liked BlueShadow's moveset for Feraligator, I'd still recommend something more along the lines of Scizor with a Scope Lens. Teach it Sword Dance, Fure Cutter, Slash, and Counter/Hyper Beam/Aerial Ace/whatever.
And for Gengar, Hypnosis only has a 60% accuracy, so it's not repliable at all. It's all on preference, but I don't even like using those power moves (thunder, blizzard, hydro pump, fire blast, megahorn, etc) that have around 80 acc, because you just can't rely on them, and moves like double team and such become a loooot more effective. You'd be better off going with Psychic and something else, I think. I'd try one of two move sets. Confuse Ray, Protect (use with Confuse Ray to stall for time after using Perish Song), Mean Look, and Perish Song (breed for this). If you're not very patient (especially since the above move sets make it slower to level your Gengar up to begin with... >_>) would be something like Psychic, Thunderbolt, Giga Drain, and a 4th move you like. Keep in mind that Gengar has a high special attack, but low attack. And ghost moves are attack based, not special attack.
Mistreavus, I'd use with that Confuse Ray, Protect, Mean Look, and Perish Song set, since her stats aren't really all that great. She learns all but Protect naturally.
And for Arcanine, well... Arcanine can't learn much except Fire and Normal attacks, so I'd recommend using another Fire Type instead, if you're using it because of it's stats. He's a good candidate for Overheat, since the only special attack moves he'll use are fire types anyway, unless you don't like the move. Well, I guess there's Crunch if you breed for it. Arcanine has enough speed that it could get away with a Bite/King's Rock (60% chance of flinching for the opponent every turn, so long as you attack first) lock, so consider that.
Flamethrower
Secret Power (Use it for the additional effects. Similar to Body Slam.)
Dig
Bite (use with a King's Rock)
I hope this helps. ^^
