Cersei is nuts and her decisions just don't work. Blowing up the Cept was stupid. You don't kill a bunch of innocents to take out your son's wife (and frankly you don't even kill your son's wife at all). She would have been much better off taking out the Olena. With her gone, Margaery would have been much easier to control.
Her actions led to the Tyrell's betraying her and destroying the relationship with her most powerful ally. That in turn led to the Tyrell's being wiped out by her and the Tarly's being wiped out soon thereafter by a more powerful force. Randall Tarly was a great general. There is now no one that can realistically control the Reach and all the best candidates aren't on her side. Dorne is also leaderless. With the death of her son, the Stormlands have no leader. She basically destroyed all of the ruling houses in the South with a couple of stupid actions. Without strong leaders, she won't be able to control those territories.
Paying off her entire debt to the Iron Bank was stupid. The Iron Bank now has no connection to Cersei. They can turn on her for a better option at any time. It might not be for Dany, or it might be. The Iron Bank supports the winner, especially when they have no skin in the game. By paying off the debt in full, Cersei took the Iron Bank's skin out of the game.
She has now alienated Jamie with her blatant lack of loyalty. The one person that gave her the support she needed. She is basically just left with Qyburn and the Mountain. She has no other advisors and they just do whatever she says. She needed Jamie's heart and conscience to have any shot at keeping power. She also needs his military reputation.
Euron doesn't have a 1000 ships. There aren't that many Greyjoy's to begin with and Euron lost a bunch of ships to his niece and in battle. He certainly has the best ships and is the best captain, but this won't be a sea battle and they won't be able to take out a dragon from the water. When the real fighting happens it will be on land and Euron's sea advantage will be worthless. The Iron Islanders are credible land fighters, but they just don't have the numbers to be of much use.
Jon may be a Targaryen, but he is also a Stark. You can't just ignore that part of his birth. He was raised in the North and grew up a Stark as well. He also has plenty of support among the northern lords (as well as the free folk), who will all follow him when the White Walkers start marching. Jon isn't stupid at all, he is loyal and rigid, but he also makes the tough decisions. He is pretty one tracked with the dead at the moment, which takes him away from other things. Jon also doesn't want to rule. He would absolutely support Dany still even if he is the rightful heir and she is not. That said, in a peaceful world, Jon is the perfect leader. He will listen, he cares, and he is genuinely a good dude. Cersei and Dany are not. They are far better getting to power and keeping power then actually ruling. You can't effectively rule a peaceful world without heart and neither really has heart.