I think if you want an idea of the max potential of Lars Eller, look at Travis Zajac. Zajac early on was pushed into a top six role and pulled off a few good seasons, but eventually it was clear he didn't have the skill to consistently handle top six duties and fell to being a low 40 point centre. Patrik Berglund in St. Louis comes to mind too. He had that hot start rookie year and his 52 point campaign in the top six but otherwise couldn't handle it.
So sure, in hindsight, it would have made more sense to move Desharnais to the wing and try both Galchenyuk and Eller at centre with Plekanec after 12-13 and see how far they could go in scoring roles. But in hindsight it also made sense to realize that Desharnais and Eller were both not good enough to be top six centres, and Plekanec was a 2C bandaid carried by Pacioretty, and that the club needed to go full throttle behind Galchenyuk, and find another centre even if Galchenyuk became a high scoring centre. So even at a best case scenario, maybe Eller plays 2C/3C with Chuck and Plekanec, but it's still not the answer for the club. And when his next contract comes, it still makes sense to move him for draft picks and bring Danault into the 3C role instead.
(And yes, Danault ended up playing 1C, but that doesn't mean it wasn't the wrong move to trade Eller.)