First clarification: I DON'T want to talk about guns, swearing, "ow the edge", overall bad reception and how it affected Shadows personality and how people view him. If you wanna discuss it, I suggest making new topic.
What actually interests me is existence of Black Doom. How making Shadow half-alien affects his status. Is it really that bad addition or is it just perceived negatively by general connection to bad game?
The way I see it, it affects those areas
1) Thematic World Building
If you watched this review you may see that people find adding aliens kinda ridiculous (Johnny didn't complained about Wisps, but I guess 5 years of Werehogs and talking Swords make a lot of difference). Admittedly I see how franchise that focused on Super Animals, Magical Stones and Robots, suddenly adding Aliens in core game feels weird. But ultimately I find that a positive. I think Sonic benefits from larger and fantastical word (to avoid Star Wars like stagnation) as long as every new addition is build to work with Sonic (to avoid lack of cohesive world, like Marvel/DC comics). That is somewhat a failure as Black Doom might be first Sonic character that looks like he belongs in different game.
And going back to Shadow, the "WTF aliens?" actually seems very fitting. Before that he was Government Military Project from Space Colony, so basically Area 51 material. It's kind of Sticks-the-Badger logic that somehow makes sense.
2) Shadow's identity
Shadow was made as A military weapon to kick ass B vague cure for illnesses C (side effect) actual emotional being and friend to Maria. Existence of Black Doom adds D alien's secret weapon E first line of defense against aliens. Somehow it muddles even further who he is, why simultaneously giving him a clear goal. In SA2 he was a weapon of destruction, but his friend Maria gave him new path of heroism. Shadow-Game says he was always meant to be hero, at least by one of his dads. So surprisingly it doesn't changes his core moral dilemma, but maaaaybe shallows it a little bit.
Of course now he's an alien, not... well he was never mobian to begin with. I don't think it changes him too much. Archie Eclipse proves it's actually interesting angle, adding another dilemma to his life.
3) Gerald's personality
Before ShTH, Gerald presented as good person, but how much proof we had for that? He worked for Gun, created weapons, was related to Eggman and seemed to only care about Maria and no one else (and that's before whole insanity-kill-all-thing). There were a lot fo shades to him. But events of Battle and ShTH make it clear: saint, saint, saint. So that gives us image on very good man that got wrapped up in between 2 evil factions (Gun, Doom) that he needed to save his granddaughter, played game of lies and deception, and he lost in almost every possible way, with Shadow being his last positive legacy.
I'm fine with this angle. If anything, I find it even more fascination that original vision, which was somewhat more muddled.
4) General tragedy
SA2 is leaves a lot untold, one of main questions being why GUN attack Ark. Without any answers, tragedy is caused by military being assholes. Now ShTH adds little plotholes here and there, but none of those matter in long run. in exchange we have implication what happened: Gun learned about Aliens (presumably from little kid Gun Commander), so they assumed everyone on Ark is potential traitor to human race, and if Gerald tried to explain they just didn't trust him. That means tragedy has more of a Ancient Greek vibe: Gerald, kid and GUN all thought they doing the right thing, but their actions lead to senseless deaths. Gerald is still a good person and yet he's partially to blame for what happened.
ShTH has a bad story (mostly because it barely has any) but larger implication create more fascinating picture. Arguably it muddles the original story, but SA2 was never straightforward. It was complicated, left many holes to fill and only character that knew all answers was dead and insane. As strange as it sounds, I don't think ShTH destroys any of the main ideas of that game.....unless you care about subtle implication from SA2 that Shadow might not be real Ultimate Life Form. ShTH kinda breaks that idea or at very least muddles it a lot. But I don't think most people care about it.
I would love to hear what you guys think.