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I have not read the books, but I know that
Varys wants to put Aegon, not Daenerys on the throne.
Since we know that
Jon Snow is now the son of Rhaegar (HBO final episode),
won't he get the push to be the new King with Daenerys as his queen? Wouldn't that solve all the lineage issues, claims to the throne, and unify everything?
The books and the show have diverged pretty far, especially when it comes to Aegon Targaryen, and will likely never match up.
As far as we know, Aegon Targaryen is not alive in the show -- we've seen no hint that he is hiding anywhere, and Varys has always openly supported Daenerys . This is most obvious in the last few episodes of Season 6. The entire plot thread where Tyrion meets Aegon was skipped completely, and Dany, not Aegon, is about to make landfall on Westeros with an army.
In the books, on the other hand, Aegon Targaryen is still alive, and he has a more legitimate claim to the throne. He's also already in Westeros, and the people in King's Landing (well, Kevan at least) are aware of him and suspect he might be telling the truth.
There's no way that Aegon and Jon can be the "same" character, for several reasons:
There's no indication that the books are going to "sync up" to the show in this regard. It would be near impossible to take the story arc that Aegon has been following and somehow "merge" it with Jon's at this point. Most likely, the show is simply going to ignore everything about the Aegon plot and go their own way. (It's also possibly -- indeed, in this series, likely -- that Aegon just outright dies and the whole problem goes away. We'll find out eventually.)
No the books and the TV adaptation are heading in completely different directions because the Show is well beyond the last Book A Dance With Dragons and the next book won't be releasing anytime in the foreseeable future.
Jon Snow in no way equates Aegon Targaryen in TV Show's universe. TV adaptation does not include Aegon's story and it doesn't seem like they would be doing it at all because in Season 7, it will be plausibly too late for that arc to be included in the broader picture. In any case Jon Snow does not equate Aegon because:
1. Aegon has support of Golden Company. Jon doesn't.
2. Aegon's first military campaign was aimed at House Baratheon of King's Landing. Jon on the other hand is focused on the North and is currently crowned King in the North.
3. Aegon is son of Elia and Rhaegar while Jon is son of Lyanna and Rhaegar.
4. Varys is devoted to Aegon in the books while in the show he is completely devoted to Daenerys and is currently accompanying her to Westeros.
5. Aegon's first major military conquest was Storm's End while Jon's is Winterfell.
6. Aegon might in fact not be Rhaegar's son after all. See my previous answer in this regard here.
That does not mean show has not done anything like that. Edric Storm's role was given to Gendry in TV adaptation but there is substantial evidence in support of this claim as many things which happened with Edric were presented to have been happened to Gendry such as:
As you can see, while one can easily see how Gendry = Edric in Show adaptation, there is nothing which suggests similar relationship between Jon and Aegon.
That would be speculation as this is about future works. It isn't unlikely and Daenerys would be predisposed towards the idea as she needs loyal allies on mainland Westeros.
In any case, Since Daenerys has three dragons, she might not be that much bothered about a marital alliance as she's got all she is going to need. She is equipped with everything her ancestor Aegon the Conqueror was when he conquered the seven Kingdoms with a small army, a fleet and three dragons. She is however lacking two dragonriders.
If it is revealed and somehow proven that Jon is in fact her nephew, she might be more than willing for the marital alliance provided they share the rule or Jon adopts a junior role in administration (Something like how Rhaenyra's consort Daemon adopted only the title of Protector of the Realm and was never referred to as King). Jon would then be the second head of the dragon.
No, it would not.
But the thing is, as mentioned on another question which I can't remember, there is no Supreme Court of Westeros to enforce the law. Might is right.
The problems would still exist because:
Even if Jon is proven to be a son of Rhaegar and Lyanna, he will still be a bastard as there is nothing to prove that Jon was born inside wedlock. He will need to be legitimized by a royal decree to assume the Targaryen or Stark name. Daenerys can do that as Queen of Westeros.
But first, this has to be revealed to people of Westeros that Jon is Son of Lyanna and Rhaegar. Only two people know this who are Bran and Lord Howland Reed.
No, not really.
Those who are against Targaryens or Starks will oppose their alliance anyways but they can be forced into submission easily because, you know, dragons.
In a feudal society, it is certain that there will always be some aristocrats who will be against the monarch. A perfect monarch who is loved by everyone has never existed.
Targaryen dynasty was not unanimously loved or supported even before Aerys II's coronation. There were many revolts and uprisings against the Targaryens which include:
Unification is something which is perfect and perfection does not exist in a universe whose arch-stone is characters being grey.
A common enemy can however provide a temporary unification. As it happens, there is a common enemy in shape of the White Walkers. Northmen appear to have utmost trust in leadership of Jon Snow in wake of his victory against the Boltons. Daenerys' own men have the same feelings about her, probably even stronger. But for other Lords and peasants of Westeros, both Daenerys and Jon will have to prove that they are the leaders behind whom the whole Westeros can stand together.
Update for Season 7
In Season 7 Finale, it was revealed Jon's real name is Aegon Targaryen. Also previously it was revealed that Rhaegar got his marriage to Elia annulled and got married to someone else who can be none other than Lyanna. That makes him legitimate.
1. Queen Rhaenys was killed in action along with her dragon Meraxes
2. King Daeron I was killed in action.
3. King Maekar I was killed in action.
4. King Aerys II was killed along with his heir Prince Rhaegar and Rhaegar's children.
The short answer is NO, simply because
Aegon has not been introduced in the show-universe.
