Winterfell's Revenge

This was the second episode ever without Peter Dinklage, maybe the third. The first was Episode 7 of Season 1. There was supposed to be a scene with him and Bronn leaving the Eyrie but they moved that to the next episode.

Every season he's not in one episode.

OK...

1) Jon's a Night's Watch member. He will not be absolved of his duties should he be Lyanna and Rhaegar's son. edit : do we know for sure Lyanna was pregnant with Rhaegar ? There are several theories on Jon's mother...

2) Even If so, unless Lyanna and Rhaegar were married, he's a illegitimate son and heir to... nothing in particular.

3) Robb contemplated making Jon his heir. I still think Jon's fate is tied to Winterfell/North, not the Iron Throne.

4) His last chapter in ADWD , he was getting stabbed repeatedly...it remains to be seen how and if he gets out of that one. Warging into Ghost isn't much good if you don't have a body to get back to.

5) Remember Ned's prayer in ADWD about the "two growing up as brothers and his lady wife forgiving him". That, along with the fact his wolf is also related to the other direwolfs, makes me think Ned is the father.

6) Only in the last published book, ADWD, we got Aemon introduced. You really think anyone else with as much as a speck of Targ blood is coming forward in the final books ?

None of what you have listed has any bearing whatsoever on the theory. Everything you have listed indicates that you have trouble envisioning what comes next should the theory be correct...which is different than the theory itself. Hate the theory all you want, but none of the misgivings you presented argue against it in a meaningful way.