You guys had me looking up Howland reed theories last night. Unfortunately two of the most prominent, widespread ones both seem to have been knocked aside by the finale. One theory held that Reed had returned as the High Sparrow, causing problems for the Lannisters that way. Although interesting, it seemed a stretch to me, and since he just died, as did everything he built, it seems unlikely they would now suddenly reveal "oh by the way, that was the Howland Reed."
The other is that Meera is Jon's super secret twin sister. The idea is Lyanna had twins and Ned took one and Reed took the other. Apart from Howland being at the Tower of joy there was little evidence for this except that Meera happens to look a little like Jon, and there were apparently off-screen hints she has a bigger role to play than we would think. There is also the 3-headed dragon prophecy to be fulfilled so people want to find the third head assuming Jon and Dany are 1 and 2. I never could find anyone explain how Meera is deemed true born. That would require that Howland confide in his wife and she went along with the charade, which is possible, but then sharpens the question of why Ned kept Catelyn in the dark, which was very painful for her. That's always been a question, but could be answered by saying his oath required he tell nobody and he held to that. But if Howland told his wife Ned just looks cruel.Anyways, since Bran saw Ned go into the Tower alone and get one and only one baby this theory is pretty much dead, unless you want to assume that some other midwives secreted Meera outside through the back door while Ned went in the front and gave her to Howland, then Howland rode off before he and Ned could ask each other "where did you get that baby?"