Illifer, I never have more than one piece of evidence upon which I build my house of sand. I don't neccessarily think that Arya will be Queen, but I think that if Mirri's prophecy of Dany's infertility is correct, then she'll need a surrogate to bear her children... a female consort, if you will. Other posters are now groaning because I've posted this before. As you've already said, Arya will get no support from the North... so all her support would come from Dany. Jon seems to be a somewhat logical choice as Dany's male consort (the Dragon has three heads), so given his comments to Arya regarding different paths leading to the same castle and remembering all of Jon's romantic feelings for Ygritte ended up with comparisons to Arya.... then I don't think it's completely preposterous for Arya (the new and improved Lyanna) to take down Cersei.
But you've brought up a great point that the valonqar and the younger queen seem to be working in conjunction. So mayhaps we should be looking for the logical connections of girls to Cersei's brothers...
Jaime and Sansa. Can Brienne fulfill her quest and bring Sansa home or perhaps back to Jaime?
Tyrion and Dany. This seems the most obvious choice. Tyrion is headed to meet Dany now. Plus, I personally love the much pooh-poohed idea that Tyrion is Dany's ******* half-brother.
Tyrion and Arya. If the above scenario I laid out happens, trust Tyrion to be greasing the wheels.
Tyrion and Sansa. They are still legally married, even if both are hiding in exile. Many people are convinced that Sansa will overcome her childish fantasies of happily ever aftering with the most handsome and gallant knight and will embrace a disfigured man viewed as a monster... Tyrion or Sandor.
As for Tommen, I think he's in real danger. Yes, the Lannisters and Tyrells jealously guard him... because he's their only hold on the throne... their only hold on a united Westeros. If Tommen dies, who will sit the throne? One of Tommen's cousins... Daven, Martyn, Lancel? According to the law, Myrcella may not inherit the Throne. If Tommen dies, Stannis benefits... actually anyone who wants a disordered kingdom or an end of interference from KL will benefit. The Starks, Littlefinger, Dorne, the Iron Islands (Euron and Asha), Dany... the weakening of central government would also benefit the Faith of the Seven.
Do I know of any current plots against Tommen? No, but...
If Tommen dies, Dorne can proclaim Myrcella as Queen and bring the Lannisters over to their side. Where is Sarella and what is she doing?
If Tommen dies, can the Lannisters really deny Stannis' claim any longer? Melisandre's magics have a long range.
If Tommen dies, unified opposition to a Free Cities' financed invasion by Dany (allied either with the Iron Islands or Dorne) has a much better chance of success.
Of course I don't have any definitive answers or even guesses... I like to just discuss possibilities... I hate to be wrong.