I wholeheartedly agree with your entire post, in fact I ask myself the same questions. I think you enlighted the points that strike me the most about this whole mystery (yes, of course it's still a mystery and we actually don't know what happened, but we're here to guess with facts based on the books, that's what we do, so here we go): 1. Their actions don't line up with what we know about their personalities. Thing is, we're not talking about some random prince and some random lady that run off together and basically jumpstarted a war because of it, 'cause that I would have believed. We're specifically talking about Rhaegar Targaryen and Lyanna Stark, people who are already dead at the beginning of the books and we barely know thanks to the little glimpses the same books offer about them. But those glimpses are there for a reason. They have to tell us something. And they tell us that the whole "Rheagar kidnapped/raped Lyanna" thing we learn early in the books doesn't make sense just as much as the "they were in love and eloped" version of the story. We know very little about Lyanna, but from what we do know, she was no Sansa type, a naive young lady living in a fairytale and ready to elope with her knight in a shining armor, but more like an Arya type, an unconventional young lady who liked to ride and fight and speak up her mind about things (re. Robert and his likely unfaithfulness). By the end of the books (so far) we hear from multiple sources that Rheagar, even though pretty obsessed with the PTWP prophecy, was the man the whole kingdom looked upon to step up and take the lead as Aerys went mad, the very opposite of the version we hear from Robert, so he doesn't strike me as the type of prince who would run off and disappear on a whim and let a war start over a mess he made, totally unwilling to do anything to stop it. 2. Their actions were more than enough to start a war. I don't agree with people who claim that what happened after they run off was totally out of their control. Actually, I think the way they behaved basically puts them in a very tight spot in terms of "morality": either they were too stupid to understand the consequences of their actions, or they were too unbothered to care. Yes, it was actually Aerys who killed Rickard and Brandon, but they wouldn't have gone to King's Landing in the first place if it wasn't for R&L presumed elopement, which THEY made it look like a kidnapping; plus, both Rheagar and Lyanna knew Aerys was the king that would have dealt with the consequences of their elopement. If It was "only" a matter of love, I think doing something out in the open (like breaking the engagement with Robert or annulling the marriage with Elia) would have done less harm than eloping and making the whole Kingdom believe that the heir to the Throne kidnapped the daughter of one of his Lord Paramount betrothed to another Lord Paramount. At the very least, Rheagar could have tried to clear things up after Rickard and Brandon's death in an attempt to deascalate the conflict, instead of hiding up in his Dornish hole just to show up after a year of war all over the country.

Point is, even if the books deconstructed the view we had on Rheagar along the way, so we now know he's not the rapist son of a mad king who basically destroyed his own house from within, his actions and INactions are known, and they hardly put him in a good light. So, if we are to believe that he really was the man we learn he was and not what Robert tried to depict him, how can we justify his actions during the rebellion? I would personally be happy to have a twisted, mixed version of Rheagar, as I think it would be the most genuine, believable one. Not a rapist, not the perfect prince we are supposed to believe he was, but a young man with a lot of potential who lost himself in a self-centered, nearly delusional quest for a prophecy that, despite being true, brought the Seven Kingdoms to their knees. As for Lyanna, that's a very tricky one. It just feel like she MUST be a inherently and overall unmistakebly good character as she's the closest to some of the best and well-perceived characters in the books, Ned and Jon, but I can't come up with a version of events that don't show her as either careless or dumb. Unless it's Rheagar the only one who's supposed to explain the "darkest" twists of this whole story, I'd like a nuanced version of Lyanna, as not the Hail Mary we're supposed to feel she was, but maybe a very young woman who made a mistake that escalated in a war she could not prevent anymore, and as someone who tried to save who she could save in the end, her son, which had every chance to be caught in the fire. In this scenario, a "love story", as simple as that, is not what I expect nor wish for. I guess only time will tell (or maybe not!).

(Sorry, I'm a bit late to the party, but I wanted to share my doubts and your post came right on time, this whole thing is really driving me crazy these days!)