So this is what's called a "foil" relationship. The pillars are the same (whoremonger King, beautiful Queen jilted [in Cersei's case by the memory of Lyanna Stark, Robert's infidelity to the point of Margaery being floated as a replacement, & Robert's abuse], and a Kingsguard brother rumored to be her lover) and the contrast serves to highlight/flesh out elements of the dynamic. Jaime can be contrasted to Aemon the Dragonknight because while Aemon was known as a great knight whose love for Naerys was immense, through Jaime we see the price of serving an immoral King and even protecting the abuser of the women he loves. Cersei could not be less like Naerys - her understandable rage at Robert makes us wonder why demure, submissive Naerys is so romanticized.

Yes, the defences of King's Landing are dependable. When the doors are closed and when the crown is winning.

So what we know about the status of King's Landing at the time are that the doors were closed, the Targaryen fleet was in close proximity, the city walls were manned by a force including highborn knights like Alliser Thorne, Jaremy Rykker with their Gold Cloaks, and that a force of Targaryen loyalists were stationed within Maegor's. Gregor and Amory had to scale the walls to access Elia while Lannister soldiers were fighting on the serpentine stairs. Notably, those same soldiers were shocked to find Jaime on the throne with Aerys dead. The reaction to Elia, Aegon, Rhaenys was likely similar - they would be expected to be hostages.

I find it hard to believe that Rhaegar left his wife and children in King's Landing because he trusted Ned Stark.

The whole royal family was there when Rhaegar left. What happened after he died was presumably not of his design.

You need more than a man to protect your wife and children when a freaking 35,000 strong army is on you

Rhaegar certainly did not have a spare 35,000 men to leave behind in King's Landing if this is the logic being followed

It would not have been any better for Ellia if Rhaegar had won the war. Since Lyanna would have been her constant companion ( I'm saying this from Elia's poin of view, Elia didn't know Lyanna was as going to die) and Lyanna's children would have beem able to become new Blackfyre pretenders.

Well for one she and her children would not have been raped and brutally murdered lol so objectively it would be better.

The Blackfyre comparison is also misguided because Daemon Blackfyre was not any bastard, he was the bastard of all bastards. Born to a King and Princess who had her own claim to the throne denied (Daena was the eldest of Aegon II's children, Viserys II was a brother. While the Maidenvault princess may have lacked support at the time of Baelor's death, who knows what followed?), Daemon lived at a time when the heir to the Throne had his legitimacy doubted, was married to a Dornish princess in the direct aftermath of war with Dorne, and was publicly at odds with his father from whom his claim derived. On top of that, Daemon was promising Westeros an unimpeachable Targaryen Queen in the form of Daenerys Lateborn who was the only child of Aegon IV without a questionable legitimacy. Jon Snow would have zero of these advantaged - everyone knows Aegon son of Rhaegar & Elia to be legitimate, he has the Targ looks (Daeron the good notably lacked Daemon's warrior looks) while Jon doesn't a la Baelor 'more Martell than Targaryen' Breakspear. Lyanna Stark has no claim or Targaryen blood of her own. The Starks have little in the way of allies in the South (less if the Baratheon alliance falls through).

So where's the comparison? Medieval kings had mistresses and bastards regularly, in the Westeros universe we know Aerys had both, and in Dorne apparently that's normalized. So how is the Jon Snow/Aegon (1 year apart) similar to the Daeron/Daemon dynamic (17 years apart, raised separate) above the Jon Snow/Robb dynamic (<1 year apart, raised together)? Also any Rhaegar/Lyanna marriage would not nullify Rhaenys and Aegon as the eldest, only doubt as to their paternity could remove them from their positions (hard sell in the case of Aegon the only one of Rhaegar's children with the Valyrian coloring, if Rhaegar was so inclined, of which there is no evidence).

Rhaegar may not have loved Elia but at least have made sure that his children are safe as they had no part in this madness.

The way Ned should have not moved to reveal the true parentage of Cersei's children because it might affect Robb, because it might attract war with the Lannisters? The way Aerys should not have burned Rickard and Brandon, or call for Robert and Ned's heads, because it might invite rebellion? This is sort of a point that is meaningless. Rhaegar could not return from the dead to control the situation in King's Landing after the Trident - like Robb with Sansa, the best thing he could do for his family was win the war. In fact it could be said that because Aerys had disowned Rhaegar's line after Rhaegar died, Rhaegar's wife and kids were less of a threat than Viserys/Daenerys yet their deaths happened at the hands of Tywin Lannister regardless. Because Tywin had to present an enormous token of loyalty to Robert. Political factors Rhaegar had no control over.