Here's my theory, a fairly common one with tons of permutations in fanfiction and so on, but usually based off contextual clues from Canon.
@DragonParadox, you can feel free to chime in on this if you want.
Brynden has been manipulating things for years, and honestly he is so used to using a light touch here, dream visitation and warging are
both things he had access to, at the very least, before magic came back fully. That's plenty--he's a social manipulator with the best of them.
He visits Howland Reed in his dreams, tells him about this great prophecy, how things had to go a certain way, and provides him with just enough information and clues and motivation to be his triggerman. Howland becomes a badass from a young age and learns how to frame his responses and reactions from the best of them. He then uses Harrenhal to manipulate Lyanna into catching Rhaegar's eye--Rhaegar who Brynden was manipulating toward certain ends, perhaps not to intentionally kill off, but probably to start a war that would get rid of some of the obstacles who have been getting in his way to having a board capable of defending against Winter in less than two decades.
Here's where it starts to go wrong.
The Tyrells sit out the war, and Tywin comes in to clean house after the rebellion. Given what Brynden knew at the time and what happened, we can surmise that he believed he could deal with Tywin later, so long as Rhaegar didn't die. Broadly speaking Tywin was hedging even before Mace started grooming his own hedge.
Rhaegar dies--by this point we can surmise he was an earlier failed project of Bloodraven's like Euron, just in a different way, hence why he was convinced he was no longer PWWP but instead his kids would be. Brynden is Team Targ, but he's always been more loyal to the House than King, and would likely point toward the fact that not all of them are going to do the best thing for House Targaryen--and would be right, since that's generally true given previous rulers he's counseled and also watched rule for multiple decades in the North, steadily losing more and more power.
Bloodraven starts doing a cover up and preserving assets. It's no longer important for Howland to hide his capabilities--he spends the war keeping Ned alive and kills Arthur Dayne to keep one of Bloodraven's future potential tools alive--Brynden doesn't know who's going to be useful and who's not.
This is all information that would take a lot of paranoia and suspicion and--at present--baseless accusations for Viserys to ever think up himself. The only way I surmise we'll learn it is encounter Howland and watching him slip up in a massive way, or being taunted with it by some Power who saw Bloodraven's hand in everything... and we'd probably not do anything about it. Because the past is in the past and we can only work with what we've got.