The big thing I think is that the Catalyst provides an actual outlet to hate on, since we actively interact with him and he's the one who introduces the Crucible. The Crucible by itself is an inanimate object, making active disdain kinda difficult/not as satisfying to complain about. The Catalyst is also the one who tries to frame those decisions into his moral scenario of Organics vs. Synthetics, which for many players didn't work.
Personally, if they had removed Synthesis which is imo just straight up weird, focused more energy on exploring the Destroy vs. Control theme, I think the Crucible by itself could have been workable, or at least as workable as possible in the confines of ME2/3, which caused quite a few problems.
So you say people hate on the Catalyst because they are not satisfied if they'd hate on the Crucible? 
Maybe I don't get all the hate for the Catalyst because I don't think it is letting you choose, rather it is also forced to accept the Crucible changed it like the dialogue suggests, and it as well as Shepard has to go along with these changes. Otherwise everything stays the same, the cycle continues. I am also quite convinced the Crucible has the tubes for Destroy and handle for Control attached to it because it doesn't make sense the decision chamber has these choices built onto them; the Catalyst doesn't even want them.
And while Synthesis is weird, yes, space magicky, I think it is only a lucky by-product because of the Crucible's massive amount of energy (which would tie in with what happens if it is severly damaged with lower EMS where Synthesis is not available) and that no one knew this would happen.
In short, to me the Catalyst plays the role of an observer who does not let you choose, but presents you the Crucible's choices to its best knowledge. Of course it promotes Synthesis, it is what it desires most after all, but your Shepard can deny it, so it's not a problem for me personally that it's going there.
So, while people can dismiss the Catalyst's talk as BS, which is fine to me, why is there need to hate it? Are people hating everyone they don't agree with? (Sorry, I guess you can't really answer this for me, but this is what's on my mind in this regard
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Well the Crucible is just this big unknown until the Catalyst explains it. There's also a psychological effect. While I think it's a stretch to truly call the Catalyst a "character" because of its limited function, screen time, and depth, the fact that it takes a form of a person gives the mind or emotions something to focus on where the Crucible is a thing.
But why is it one or the other? I hate both and many do as well.
Fair enough if you do hate both, but it made me wonder why many people do not hate on both. Especially since a lot I've seen here points to hating the end choices = must hate the Catalyst. If the Catalyst is removed, some people are happier with their ending. Why is that? The Catalyst removal changes nothing from the core game or the decisions, but they are fine with the outcome then. This is what's curious to me because obviously the Catalyst is just as trapped by the Crucible as is Shepard, and still it gets all the hate; not from you as you already said, but I've seen plenty others, and use of the condescending names like Starbrat etc just show how much they hate it and I don't know why that is. It might be as you guys say, they can project their disappointment and blame it on this one "character", but that's just an emotional reaction and no real reason to hate on a character imho.
And what makes Shepard qualified to make this choice? Harbinger's poor aiming skills? Shepard didn't build the Crucible. heck Shepard didn't even find the plans, Liara did. All Shepard did was play errand boy for Hackett and creep on some conversations on the Citadel. Where's the Crucible team on this? Hackett? Victus? The Council? The galaxy built the Giant Magic Space Wand, but Shepard's the only one who gets to use it? Without even a couple of companions to play angel and devil on Shep's shoulders?
You might not see Shepard as qualified, but Shepard has experienced every theme tied to the 3 choices, had the opportunity to directly work with all races and see their stances towards other species because he/she's the one who united them and had to deal with their BS. Many of them still hate each other and I think I can see them all going for Destroy anyway, except Synthetics obviously. None of those races have experienced what Shepard did throughout the games, so I do think each Shepard can count as qualified in a way. Shepard has seen TIM with Control, had a chance to either become pro-/anti-geth, pro-/anti-quarian or can work out a truce between those fractions, giving both fractions a chance, and has seen enough of the Reapers to make up their minds if they still want to have them around or if they want to play safe and get rid of them.
The fact that only Shepard is able to use it is probably tied to the great plan to only have a handful of people go and try to run for the beam so that one of them could open the Citadel arms. No one anticipated that any more would be necessary than to open the arms. If we consider this, then well... Shepard's just at the right place at the right time. Because Shepard is the main character and the last choice is there for the players to make, simple as that (yes, I'm aware that many don't like the choices, but that's how I see it). Actually, I'm quite in favour for what sH0tgUn jUliA said below, about the ending being determined for you. But it might gather hate regardless because players could feel control over the end is taken away from them. You can never satisfy everyone.
Or maybe you get multiple endings, but you don't get to choose them in the end. Maybe your actions throughout the series determine the way the story ends. They can do that stuff. If you want the good ending, maybe you shouldn't kill _____ during the game, or maybe you shouldn't side with ____. Your choices matter.
I like the idea of having multiple decisions/actions lead to an ending for you (similar like the Rannoch or VS choices play out). This would maybe also encourage loads of replaying.