I think Martin really likes developing background more than telling the main story. As a result, we all see red herrings every turn. Meera theories are probably over thinking it IMO
Well, maybe. But, I'm not so sure.
It always struck me as very strange that Howland Reed would send his two young kids to Winterfell while The War of the Five Kings was ongoing. Why? It would be more likely, if he were to send his two young children (and only heir) on a long journey, through a land at war, that he would send them under the protection of an entourage of fighters, (or if he wanted them to not attract attention, send at least 1 bodyguard with them). Now, if GRRM had told us that they ran away, I might buy that. But, he has never really explained why they showed up at Winterfell.
To me, this suggests that he needed to interject them into the story for some reason, and needed them to be part of Bran's entourage for some reason (i.e. so the reader could get to know Meera as a character). Bran's story doesn't need Meera. He could have been accompanied by anyone. It could have been the Winterfell blacksmith's son, or an apprentice baker from the kitchens.
I won't be surprised if the Meera theory turns out to be fanboy BS, but something just doesn't add up about her and Jojen. Either their backstory is one of the weakest parts of what GRRM has written in ASOIAF, so far, or he has purposely made it murky in an attempt to catch the reader by surprise when we learn of her (or Jojen's) true significance to the story.