The 90s get a bad rap in comics, but there were some awesome things in the medium and, specifically, at Marvel in those years. Not everything was excess pouches and why do you hate pouches so much, anyway? Pouch-hater.
Larry Hama and some very talented artists took Wolverine from being an uber-violent jerk with a heart of gold to being a heart of gold who also had a lot of problems and a closetful of trauma. And, the whole time, he was still so cool, nobody seemed to notice that the jerk was gone and what we were left with was an introspective, helpful guy who kept to himself mostly because he didn't want to drag anyone down with him, and who sought out company because hey, he likes people, especially women. Larry Hama made Wolverine the moral high ground of the X-verse without ever drawing attention to it.
Meanwhile, over the course of the late 80s and early 90s, Hydra had become a goofy joke, repetitive, doomed to failure, a joke even when they were trying to genocide half the planet with a weird mega-bomb or chemical weapon. Nobody cared. Fury stopped caring somewhere between his second and fifth death in the 90s, Jessica Drew was past all that noise, and the Crippler still cared, but nobody cared about the Crippler. Cue Heroes Reborn.
Lee, Lobdell, and Portacio amped up Hydra hardcore in Iron Man. It was effective even with all its members dying, because they were just brainwashed fodder. Hydra didn't care how many of its agents had to die and if SHIELD or whomever wouldn't kill them, Hydra would just do it themselves. Suicide bomb cult led from beyond the stars or outside sanity, wherever the new Mandarin was from. And, it was scary.