Of all of those I'd say that Bayonetta the least awful due to being pure T&A power cranked up to 11 (granted Bayonetta runs on enough rule of cool fuel to compensate but that just means she's as effective as DMC's Dante but with tits), but the others listed in your post aside from Samus are so generic that you might as well throw in Lightning Warrior Raidy's and the Valis series's main characters along with everybody but the trap and the kid from Queen's Blade on that list too (for reference the first example is a porn game, the second degenerated into straight porn, and the third is the fetish fuel mecca) because aside from actually showing the naughty bits they're basically just as meaningful and well developed as Lara Croft, Blood Rayne, and the Resievil chicks. However, at least none of them are as bad as Samus because when you see the massive misogyny behind the series being laid bare in Other M that you have to wonder just how much agency was lost when something swooped in for a save be it The Baby, random Chozo Ghosts, Adam, or otherwise. Basically Samus Aran is just a terrible female character, the rest exist because sometimes gamers just want to watch females get impaled on spikes, crushed by walls, devoured, ect.
What exactly did you expect? There's plenty of female leads, and they tend to be just as shallow as their male counterparts. Its hard to find a good lead in general, regardless of gender. But for the sake of argument, also right off the top of my head, Raquel from WA4. She was the games powerhouse, she was not there for the sake of fan service. She was easily my favourite character in the game.