I wonder if it's just because people expected him to be more important than he was actually intended to be, and planned out a lot of stuff for him that wasn't ever going to happen (Kirihiko from W comes to mind here)
I don't think this is a similar situation. A lot of people saw Kirihiko's death coming, and you can argue that his death has long-term impact in W (mainly in how it affected Saeko's character). It was a well-considered arc, and the way he died-- though depressing-- basically
made sense. So people accepted that it had happened, and mostly just wished there was some way to truly redeem Kirihiko from beyond the grave, or that someone had intervened on Kirihiko's behalf.
The problem with Phoenix is that the way he dies just
doesn't make any sense. You're seeing this demonstrated over and over again in this thread. If anyone puts even more than a few seconds thought into how Haruto "killed" him, it's really obvious that the solar prison should be nothing more than a delaying tactic. Whether it's in one year or one hundred, Phoenix should be able to get out eventually. People will still accept this way of beating Phoenix if, at some point, say in a film, the narrative revisits the issue and has the heroes devise a more permanent solution to the Phoenix problem. If the narrative never revisits this plot point, it's going to become something people hold against the show, because by itself it just doesn't work.
That's why I think this is simply a failing of writing in Wizard, one that really betrays Kida's roots as a stage show writer. Nobody thinks about stage show plots, because they're primarily an exercise in spectacle. In fact, the sheer whimsy of Don Dornheiro hiring the Grongi as anti-Timeranger hitmen, prompting a team-up with Kuuga, can add a level of pure fun to the proceedings. But that's
in a stage show, a live event people go to largely to see their kids smile at the men in suits.
In the actual shows, people will still excuse a lot in the name of spectacle, but they'll expect a certain level of basic thought to go into the plot. What's frustrating in Wizard is that the writers clearly think about their plots. The story itself brings up stuff like Beast logically thinking he's the guy who could put Phoenix down for good. Yet then, these possibilities are immediately handwaved away, usually by some flimsy character-based exception. In this case, it's Haruto saying he feels like he should beat Phoenix because it's his responsibility, and Beast basically going, "Well, you've persistently failed at attempting to do this since I've met you, but okay."
So instead of what would make sense at this point in the story, Phoenix being beaten by some sort of team-up attack, Haruto goes it alone. This is clearly just a case of it having been decided by the creators that Haruto will get the kill on Phoenix completely by himself, before anyone really thought about how this could happen. So Haruto doesn't even go it alone in a way that makes any sense. He doesn't visit White Wizard to get a special Phoenix-killing magic poison ring made, Haruto doesn't even come up with any clever tricks or spells to get around Phoenix's regeneration by himself.
Haruto just... he just gets a power-up that lets him hit Phoenix harder? The stuff with the sun is just there to handwave how the hero can beat this particular villain by hitting him harder, after several episodes devoted to showing how you can't beat Phoenix by just hitting him harder because of the special nature of his powers. The show has actually pre-explained why its own plot point doesn't work! This's just bad writing, even if other things about the episode worked (and I think they did). It literally invites people to try and argue against the show's own narrative, in a way that doesn't otherwise benefit the story in any particular way.