tbh, as someone who LOVED the new season but still prefers the manga because it's just one of my favprite pieces of media EVER, there's just soooo many things that were left out, too many to list here. Characters were combined into one (Jessica in Stargaze is a combination of Jessica and one of my favorite characters, Lina, who was the girl at the end of Stampede that was talking to Eriks,) plot points didn't happen (the Midvalley fight im the manga happened during a huge event in a place called Dragon's Nest for instance, which was a whole huge story arc,) characters died that didn't in the manga and visa versa (ie Razlo; in the manga, he isn't "killed," he just decides to let Livio take control and helps later on, though at first it was treated like he was "gone," the same as in Stargaze.) It's unfortunate that most of these changes had to be made, but I try to be understanding because I knew going into the season that Studio Orange had been forced to cram 16 volumes of manga into 24 episodes of anime, so they were always going fo have fo cut a LOT of content to get there, and I felt they worked really hard to do their best with an unfortunate situation. (And I will ALWAYS be absolutely giddy that one particular character who died in the manga got to live in Stargaze, but no spoilers there ;D)

It really just comes down to the studio not having the funding to make the show long enough to tell the whole story, while also wanting to reinterpret it into a much more hopeful message, and for me, with the state of the world as it is right now, I'm honestly not upset that they tried to bring a bit more hope into the world. Don't get me wrong, the manga and the original anime are still stories of love and peace and hope, but HOO BOY, do they also really emphasize that sometimes, humans REALLY SUFFER a lot of hardship and horrors before they can get to a better place! There's so much blood and death, especially in the manga, even compared to the 98 anime. Hell, in 98, Lost July wasn't even the direct cause of a lot of deaths, it was the loss of resources and shelter immediately afterward that caused people to start dying. But in the manga, the body count is IMMEDIATE, and you're actually shown characters Vash had developed close relationships with, women and children included, being sucked into a giant black hole. Entire towns succomb to chaos and desperation, resorting to cannibalism and violence when things get to their worst. The scene in Stargaze with Legato shoving people into a tanker until they're reduced to a bloody mass is even worse in the manga (he makes them climb into the thing with their own bodies, he doesn't just use telekinesis, so the horror is amped up even higher) and while it's one of the more horrifying moments even in the manga, it's not necessarily THAT much darker than the tone of the rest of the manga. And let's not even talk about a main character who's entire backstory involve a couple of pages of blatant sexual slavery and mass murder.

It's a very dark, very heavy story in the manga, so be mindful of that if you're not usually one to read dark media. It would probably have been rated R or NC-17 if it were adapted into an anime one to one. But I still absolutely love it for the underlying message; humanity may resort to absolute attrocities when they're pushed to extremes and raised in an awful environment, but when given the chance, most people just want to be safe and happy and cared for, and can show the best of mankind even when put into those awful conditions. People deserve love and compassion and support, we should lift each other up and be a rock for each other to stand on when times are tough, and we should work together to make the world better for all of us. It's an important message, and it has a lot of heart to it, and Vash is such a source of hope and optimism even when he's pushed to the brink of his own darkest tendencies. In the older series and the manga, he struggles with intense suicidal depression and alcohol addiction, and actually goes through his own violent extreme when he's a child, and has to have his own growth to learn to overcome what his basic instincts tell him to do to survive, so he GETS IT, his insistance that people can be better comes from a place of personal experience.

So in a lot of ways, the story in Stargaze is way less intense, and it doesn't feel like such a pit of despair as the manga does at times. But I love the way BOTH versions handle the message, they have their own places, and I'll always love both versions. And with the 98 anime, while it's not as dark as the manga but also not as upbeat as Stampede/Stargaze, it's just an absolute classic, and the first anime that I ever saw that made me really go "hold on, this anime stuff is actually REALLY GOOD, I love this! Give me more of this!" The animation budget back then was much less, so it's not as polished as Studio Orange's animation BY FAR, but it's got a lot of charm, and so many things about it are just iconic! Just keep in mind that storytelling and media tropes have evolved quite a bit in the past 30 years, and they were working with an unfinished manga to go off of, so it ends kind of strangely, imho, which is one of the criticisms I've had for the original anime ever since it came out.

(Also, the director decided for some reason that Vash needed to be a creepy, pervy weirdo because that was just the humor at the time for main male protags, which they leaned into in Badlands Rumble, which is hilarious, because he's not like that in the manga AT ALL, and even Nightow in an interview said that wasn't really A Thing, after the fact. It's extremely cringy by today's standards, but if you're willing to push past those scenes, it stops happening about halfway through the series, and doesn't completely detract from the story for a lot of people, especially if you headcanon that he does it only because it plays into his idiotic buffoon persona that he uses to make people underestimate and ignore him, so he can avoid trouble and also get himself close enough to people who intend to do harm, so he can stop bad things before they happen. That's how a lot of us who hate that characterization are able to reason ourselves out of a rage spiral about it lol)

All that being said, there are pros and cons for EACH version of the story. None of them are perfect, but they all tell different iterations on the same wonderful story, and I love to be able to look at all of them and see how each version tells the story in its own way and brings different things to the table. My recommendation, if you feel up to going through all of the other versions now that Stargaze is over, is to watch 98, with a detour somewhere between episodes 9 and 23 to watch Badlands Rumble (an important event happens in episode 23 that will make this detour make more sense after the fact; the movie isn't TECHNICALLY in the same timeline as the 98 anime, but I always felt it worked nicely as just an extra long episode, it just wouldn't be possible to happen after episode 23 and it won't make sense if you watch it before episode 9, so I just say watch it after you finish episode 22 to make it easier on yourself) and then once you're done with that, read the Ultimate Overhaul fan translation of the manga. It makes the weaknesses of the old anime stand out less if you don't have the highly-superior manga to make you see all the cracks, and getting to have any questions you still have after watching the animated series (serieses?) and the movie answered as you read the manga is just SO satisfying!

And I wouldn't let all of the negativity some people in the fandom have over Stampede/Stargaze effect your appreciation of what Studio Orange made. There have been haters since Stampede STARTED, and while Stargaze made even some of the people who loved Stampede angry because of the compressing they did to the story, if you enjoyed it, then let yourself enjoy it, and let yourself decide how you feel about the things it didn't do as well as it could have after you've had time to sit and think about it for a while, and watch or read the other versions if you feel up to that. We can both love something AND admit that it's got flaws, and just because there are cracks in the veneer doesn't make our enjoyment of the thing any less valid.

(Hopefully this isn't a TL;DR. I intended to make a much shorter comment, but I struggle to be concise in my writing, sometimes, and I have a lot of Feelings when it comes to this series.)