You folks are all thinking too small here.
One of the best things to come out of writing a story in an alternate setting/dropping ahead a century or so into the future is just how NOT limited you are by the constraints of existing canon. You can literally pick and choose what you like and what you don't. You don't necessarily have to make the world grimdark/crapsack/post apocalyptic, but neither do you have to make it bright, bubbly, and oversimplified.
In writing my Starfox Fanfic, I advanced the setting 75 years into the future after Starfox 64/The Lylat Wars, and said that Starfox Assault happened, but Starfox Command DIDN'T. It gave me a chance to expand the Lylat System and explain what the fall of Andross and the rise of the Cornerian military would mean after decades; A setting in which Arwings were seen by those who refused to fall under the banner of Corneria's empire as a symbol of oppression, and there had been a 4 decades long resistance and outright intrastellar civil war before Corneria planted its flag atop the hill of their fallen foes. Then I introduced a new alien threat which turned out to be ancient Lylatians related to the simian species that were 'coming home', and threw it all into chaos again. I made the primary protagonist Fox's granddaughter, I had her brother MIA, Wolf's grandson was her Commanding Officer, and the latest Arwing was capable of completely nullifying gravity and doing a ship to pilot mental link and dropping bombs that created microsingularities. And even though they were struggling to fight a war thrust on them from the new invaders, they still had plenty of moments of happiness, joy, and laughter.
One of the best examples of the 'alternate reality' to come out in the last 15 years was from Justice League, where Superman finally got fed up enough to brain fry Lex Luthor, and he and his team in that world ended up leading a relatively bloodless coup to create stability and peace and order. Of course, then they tried doing the same to the reality of the Justice League in the cartoon show. That was where the trouble started. It not only showed what could have been, but also highlighted what the team might do if they had a truly bad day. Come to think of it, the plotline of Injustice was likely derived a little from this possibility.
So far the ideas presented here all range from Big Ideas, such as the Dark SWAT Kats show up in the good guys' reality to wreak havoc, or Little Changes, such as Dr. Zyme becoming Dr. Viper and Dr. Elrod Purvis being a normal kat. You've come up with alternate backstories for existing characters, such as Hackle being an evil mad scientist bent on conquest as opposed to his more peaceful version we're familiar with, or Mac and Molly Mange NOT leading a life of crime, but instead being former bodyguards.
There are a lot of stories out there who do things like this; They change one little detail, or alter some quality of an existing character's personality that the writer disagreed with so that in a given situation, they react differently and create an alternate outcome and future. These are known as "Fix Fics." There's nothing wrong with these, they can be quite popular, but you know what they say in the world of writing; there are no new ideas, only new combinations. Had a professor in College who loved boiling down movies, stage productions, and everything else into less than 10 stories. That's something that I have to keep track of myself; as much as possible, if such a thing is possible, anything I write these days has to be just a little bit different and beyond what others have tried. I do so hate repeating things, after all.
Let's take that idea of the Dark SWAT Kats didn't perish, but were thrown into a different reality when that bomb went off still connected to their Turbokat. Why toss them into the same world as their own SWAT Kats? If the SWAT Kats we know are considered the 'middle of the road', hurl them into the opposite extreme; a Megakat City where the Enforcers collapsed, and the SWAT Kats had to take over protecting the city...without the masks.
These two evil SWAT Kats, turned that way out of the bitterness earned from having their lives torn from them, find themselves in a world where as they're flying to try and get their bearings, they are not chased down, but are openly hailed on the radio, albeit with some confusion. They head for their hangar and find that the underground hangar's been converted into a museum. They bail, and going undercover, find that there is no going incognito. Chance Furlong and Jake Clawson are heroes, with Chance and his trusted right hand kat, Felina Feral, serving as the heads of the Enforcers' replacement, the "SWAT Corps", while Jake Clawson is a rich and brilliant engineer who makes all the gear for the SWAT Corps in house and happens to be dating the single most eligible bachelorette, Mayor Briggs. Or Hell, I don't care, switch it around. Offered a vision of the exact extreme, they find they have no reason to be who they were. They want money? They have it. They have power, and prestige as well, and they can go anywhere. There are somber moments as well; learning that Commander Feral died in the final moments of the Enforcers' existence, sacrificing himself to spare the city from Dark Kat's last suicidal attempt to tear the city apart...and that his last words were ones of confession to a revealed Jake and Chance in that reality, telling them that they were the best troopers and pilots he ever had, and that it was his own stubborn pride that wrenched them, and having realized that they kept on fighting in the role of vigilantes, he asks them over the radio to Take Up His Sword, to keep protecting Megakat City. And that that is exactly what the two former vigilantes did with the full support of what was left of the Enforcers, reorganized into the SWAT Corps, and the city government as well.
Throughout, you'd have these two bitter, rather violent and self-serving blokes start to take a hard look at their own lives, and slowly change. They stop insulting and smacking each other so much. They start to take a little bit better care of themselves. Feelings, hopes and dreams that they'd thought long ago buried and forgotten start to resurface. After all, are the SWAT Kats really beyond redemption, or were they twisted that way because of the hand they were dealt? Without a dark overlord influence like Dart Kat around, would they stay as they were, or, by seeing the lives their alternates lead, start to ask themselves; Can't we be better? A dynamic character, one which changes as a story progresses, is always more interesting than a static character, who never changes regardless of what happens.
If you really want to change things up, have the two Dark SWAT Kats be forced to step up to the plate and deliver; their good counterparts in the reality that they found themselves dumped in are threatened, and they move in to save them. Tragically, the good SWAT Kats are slain, and Felina and Callie, the only ones who know the truth, ask the 'dark' duplicates to stay on and fill the shoes of their mirror opposites. "Megakat City needs the SWAT Kats. We need you to stay." And as easy as it would be to just get back in their Dark Turbokat and try to fly off for home or someplace else, the two find that they can't. They don't want to. They've found a place that they could belong, and a place where they can find redemption. You end on a bittersweet note there, with Dark Chance finding himself as the reluctant leader of the city's police force, and Dark Jake taking over as Chief Engineer...possibly helping Callie and Felina through the grief of losing their lovers, and making those first awkward steps into building a relationship of their own.
In that way, you've addressed the alternate reality conundrum, you've created a situation full of dramatic impact and dynamic character growth, and most importantly, you've done so in a way that is so starkly different from all of the other 'Alternate Dimension' Fics out there that it stands the test of time, and leaves behind the other 90 percent of stories to join that rare 10 percent people favorite, bookmark, and recommend to others.
We want to make good stories. Don't be afraid to go a little farther to make that happen.