Not buying the R+L=J&M theory at all. At least with the current supporting evidence, which is pretty weak. There is not a ton of evidence that thoroughly debunks it, but there's also little to no evidence that it's actually even a legitimate possibility.
As far as I can tell, this theory is based only on two kids of similar age and hair color whose dads (term I use loosely considering my opinion on Jon's parentage) happened to be at the same place at the same time once. I'm not buying it. My best friend and I growing up were born days apart and both of us have blond hair. Our parents were already living in their homes across the street from each other long before we were born. Does this mean that we're potential siblings?!
Another thing for book readers to consider is that we get a pretty extensive look into Eddard's mind through his many POV chapters in AGOT. He thinks of both Lyanna and Jon often, many times in the same context. But there's never an inkling of him thinking of Meera or even a vauge "other" child. You'd think that if there were twins, he'd at least have a thought about the other one when thinking about Jon.
But hey, like I said, there's nothing to definitively disprove it, so who knows? One of the most fun parts of the ASOIAF fandom is all the theorizing.