Julia - I don't see this one either, but it's not -because- her gym was targeted for demolition per se, as much as it is that she is threatened along side the player by the Meteors after the infiltration.
Florinia - Probably not. Partially due to the same reason above, as well as partially being too busy and too much of a past character for it to really make sense to us as players. The shock value would definitely be there though.
Shelly - I don't exactly know what you guys are reading into here... The angle makes sense, but I feel like Shelly wouldn't directly be placed in harm's way and as such could depend on the player to prevent any harm to Heather. I'm not exactly up to date in-game though.
Shade - Shade seems to be an equalizer. I don't think he would shift any power to any one side, and therefore I doubt he is involved.
Aya - Put it down in the "suspect" column. Aya may -still- hold relevant disdain for Cain who is an active opponent of the Meteors. She's not one you can immediately attribute good intentions to, because she's full of self doubt and angst. She seems like she could be the "easy dupe" leader to target...
Serra - This washed up model is accustomed to losing everything she once held dear, but if she was given the opportunity to get it all back by a certain organization, -would- she? Serra is a weak female character, but I doubt she would pass on any chance at redemption that was thrown her way.
Noel - The only reason to consider either of the twins for this "betrayal" is the pure shock value it would have. There's not much sense involved here, because that would put the orphans back in the clutches of Dr. Connal.
Radomus - There's two factions with Radomus really... You either were very suspicious of his aloofness and believed a previously met character in Elias because of it, or you caught on to his cunning and appreciated it, resulting in siding with him before the battle with the Ditto-Arceus. If you thought the Psychic Leader was very aloof to begin with, you -should- suspect him. I'm -really- sold this man is either malevolent (and thus possibly involved with the Meteor plot) or a -very- slippery character by the fact that you have to GIVE Anna's pendent to him for reasons that don't really get explained by anything other than curiosity. The jewelry seems to be very important in the game, and for us to hand it over to him is enough to put him in the list. The question some of you may have though, is this. Would it be "shocking" enough? I think it would - for those that trusted him enough.
Luna - Not enough evidence to suggest that Luna would be working with the Meteors directly. She's a bit nomadic, and loves darkness, but those are too vague to attribute her actions to. She seems to have a beef with El's cult and until I know the cult isn't linked to Team Meteor more conclusively, I won't suspect Luna much at all.
Agate Triumvirate - None of these are terribly likely. Not enough known about them.
Titania - If it wasn't obvious before, then you might be shocked. This lacks shock value more than any other option, due to an event in-game that the player witnesses. I'm not going to say this -confirms- her being a Meteor, but if there's supposed to be shock value, this is not going to deliver.
Amaria - Memory Loss is a TERRIBLE reasoning behind suspecting her, unless Titania is -not- a Meteor. Amaria very recently suffered a serious injury at the hands of Solaris. That's not something that is easy to forgive and will linger even if more screws come loose. Keep in mind that Amaria is one of Shade's monitored characters (in his gym) and that the theme behind those monitored events is a clairvoyant glimpse into the death of said character. Titania -may- kill Amaria, but it's more like because Amaria will try to intervene on TM's plans than it is Titania trying to stop them. That is of course, if the inverse is true. Titania is -indeed- the good girl of the two when the dust settles. I'm not saying you can't suspect her, but her memory loss isn't a selling point to me.
Hardy - This guy is a possibility. If Aya is placed in danger and the terms of her survival include Hardy working for the Meteors, He -might- do it. Shock value? Present. Motive? Present. A good suspicion.
Saphira's clan - Nope. Not going to side with the Doctor unless it's revealed that he really isn't that much of a bad person and has new motive to suggest so down the road.
Aya. Serra. Hardy. Radomus. TItania.