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Your logic is correct about Ellie as to whom she ought to end up with. However, two things to consider, first The Blue Pill poisoning at the beach was a prank--yes a bad one that is dangerous. Sadly, a lot of pranks are not well though through and people die. And in this case, I don't think Ellie intended to kill Dylan. Second, Sophia is in the way of a Sam/Ellie route. Between Sam and Dylan, Sam's feelings are the most honest while Dylan is an opportunist. A special consideration is the developer themself; it just seems the developer is going to force a Dylan/Ellie relationship--one way or the other.
As to Dylan being a brother-- well Sophia is the mom. Hard to square one taboo relationship with another. From a logistical point of view does anyone want more time spent making a Sam and Ellie route? It's not possible but with so many story threads being killed, the odds are not favorable.
Sophia isn't in the way of the Sam branch of the Ellie route. Sophia's been pushing it, at least twice already during the showers if you're playing both Sam and Ellie routes. It's through Sophia recommending Sam instead of Logan that we learn that Ellie doesn't date younger guys. Which excludes Dylan.
And on the Sam route, after the concert there's the option to pick Ellie up at the beach after Logan abandons her. So at this point Ellie learns that Sam is a rock musician,
and has a car. Don't know what it was like when you were younger, but in my area friends with cars had prestige. Which fits in nicely with Ellie's need to look good and be popular.
A Sam branch also neatly fits into the same model of Sophia's LIs - the good guy, the bad guy, and the lesbian route. In Sophia's case it's Sam, Dylan (and by extension Aiden), then Ellie and Patricia (whose routes are so intertwined you may as well consider then one). In Ellie's, it's Sam, Logan, then Jules.
On the other hand, there's nothing on the Ellie route of Sophia suggesting Ellie pursue Dylan. Only that she stop calling him names like troll, gnome, goblin, etc. You don't even need to be playing the Ellie route to play the bonus storyline. And with the bonus storyline now being mutually exclusive to the Sophia/Dylan branch, there's little chance of Sophia suggesting Dylan pursue Ellie.
Not going to weigh in on whether or not the Sam branch should be scrapped - only that as a Jules fan, I'm not going to be playing it.
