Okay so for Aya I personally completely reconstructed my entire team to compensate and I whooped her within moments of going in with them
Sturdy Magneton: Resists poison, could set up with charge beam and pretty much slowly kill her team. I also used this to specifically kill Tentacruel by slowly charge beaming up.
Sandslash: I didn't see anyone else mention this one, but he's pretty great. He learns Earthquake at 46 so you'll have to force some common candy down his throat but he'll be awesome afterwards. Also gets swords dance, which is great to set up with, esspecially if Muk, Tentacruel, and Nidoqueen are dead. You can catch Sandshrew underneath the Grand Staircase.
Protean Greninja: There's not really much you can do to sub in for this one.
Mixed Attacker Flygon: I couldn't be bothered to try and breed a Flygon with EQ and decent attack IVs so instead I trained him up normally and since he had near perfect SpecAttack IVs, I made him into a mixed attacker. I also managed to grab him an Earth plate to boost up that Earth Power. He also had Crunch for Gengar and I think Dragon Tail to deal with Dragalge.
Meowstic (Female): Light Clay is priceless. I had it with Light Screen and a STAB attack and without it, Sandslash would have perished instantly.
And finally, the one, the only...
Shedinja. Yeah, that's right, Shedinja. The Wonder Guard menace. You can get this thing from rock smash in the wasteland to get a Nincada. After that, you can use it for a free switch in, use Screech, then Shadow Sneak or star Fury Cutter-ing if you're feeling confident. If you can kill Gengar with this thing, great. If not, you were probably still able to cause some serious damage based on how little she has to counter it.
I hope this helps. I wish there was more I could do to help with subbing something in for Greninja, but I'm not quite sure what would fit the bill. I'll do some research and get back to you guys.