I've finally watched it. I liked it, but I didn't love it. The shift in medium from live action to animation might have some part to do with it, but I do love animation as a medium, so it's not that I don't think it was a wrong approach or method. It left me wanting to see more of the inside of Babylon 5 itself than what we got. It was ultimately still an alternate realties story, and I'm still just not fond of them. The whole need to get Sheridan back to his normal reality and time or else all of existence will be destroyed is too comic bookish: it's a scale, a scope that has no weight; it doesn't feel like a genuine threat at all. I'm not against the love-will-save-the-day ending, but it was perhaps a bit syrupy, or at least felt told in a way felt like the moral-of-the-episode way cartoons I watched as a kid would conclude an episode. It kind of made me want to draw the conclusion myself rather than be told.
My favorite scene probably was the rim of existence between Sheridan and the Universe-as-G'Kar, though there was a moment where a line of dialog from Sheridan felt like he was responding to something unsaid, and it left me wondering if there was some kind of edit made late in the process; it was just a bit abrupt. I think that might be the one scene I most want to revisit in a rewatch.
The Shadows didn't feel threatening like they did in the show. They didn't have a vibe of elder beings of the galaxy, and instead just felt like any other generic sci-fi bug-analog alien. The animation of space battles felt like they lacked weight, which is kind of funny to say since they're in space, but I guess I mean that ships didn't feel under the influence of physics and inertia. I thought the animation of the character models were good though, especially for the specific animation style used.
As others have mentioned, there were some moments of "humor" that just did not work, like the self-destruct system or whatever talking back to Sheridan. The moment should have been the height of tension, and that "humor" severely undermined it. Some character encounters were too easily accepted or unquestioned. It makes no sense to me for G'Kar and Lyta to be in the self-destruct room, for example. Younger Sheridan getting Lyta to scan regular Sheridan works, but Sinclair accepting Sheridan while fighting Shadows does not--it's just sort of hand-waved acceptance rather than gained acceptance. So it makes me wonder if the scope of the story was to big for the limits of a single animated movie. Zathras became too much for me, especially the giant horde of him on the planet, but maybe that just gets chalked up to being more awkward humor.
I think the waiting for Earth's destruction scene felt unfinished or something. I know it's an alternate reality, but Londo and especially Ivanova in that scene just did not seem, didn't speak or behave like I would expect their characters to do in such a situation. I can't quite buy the two of them in the scene together in the first place. And I think a bit part of that is the nature of alternate reality stories in which you spend so little time in any one of the alternate realties. It leaves me unmoored and thus uncertain about how I should feel or what I should think about any of the alternate versions of characters. And I agree that Sheridan's experience in the story was mostly just him as observer, which the story heavily philosophically leans on, rather than as an active role in events. He's mostly just kind of there, not quite so much doing anything.
I enjoyed myself watching the film, but it doesn't feel like the second coming of Babylon 5 by any means. It did make me want to see more of Babylon 5 though, but think I'd need to have a much more strongly delineated break from the original than the let's-have-everyone-including-all-three-commanders-together alternate reality at the end would be.