But okay, let's say I wanted to change the series as little as possible, but make it as good as possible. I can't change the premise, it still has to be about Knuckles taking Wade to a bowling tournament and teaching him life lessons along the way. Well obviously Knuckles is the bowling ball. The whole thing should have been that they stop at other bowling alleys along the way and hustle their opponents to win money, but actually they're cheating because the ball is alive. And then the GUN agents figure this out, and that's how they catch up and find them at the final bowling tournament, so when they're at an actual important game, Wade is on his own because Knuckles is busy fighting a giant robot outside or whatever.
And of course Wade's dad should have been tied in more with the GUN agents, beyond just having him sell out the protagonists to them once. And there's the third antagonist of the Bounty Hunter, who is also a bowler. And "The Buyer," who is also a former GUN agent. This is all so messy. Obviously The Buyer didn't need to be a separate character. Just have it so the two primary rogue GUN agents used to work for Robotnik, and they have the same motivation The Buyer has. He is the only one who is physically threatening, though, so maybe just make him a current (but rogue) GUN agent instead and have him fill their role. There is no reason this needs to be two separate groups.
Jack the Bounty Hunter should come back at the end and become Wade's Dad's partner. Or better yet, combine those two characters, so Wade's bowling partner was his dad the entire time, and Wade knew it, but didn't tell his family that he was hanging out with his dad because they hate him so much. Then when that guy gets recruited by GUN, instead of the betrayal being that Wade's friend betrayed him, which is repeated when Wade's dad betrays him, it's all one character. Instead of one recurring antagonist who is replaced by another partway through the series, make it all one guy.
Make it so Wade has been casually bowling with his dad in secret, thinking they're rebuilding their relationship, but then when the bowling tournament comes up, Wade gets his hopes up that they can compete together, as a team, but instead his dad ditches him (again). Then Knuckles takes Wade and becomes a surrogate father figure, which is bizarrely what already happens in the series, but if you're introduced to Wade's daddy issues earlier it will make slightly more sense.
So they start on their road trip, but stop at another bowling alley on the way, for practice. Knuckles is all about honor and everything, but when he sees the alley's local bigshot challenge Wade and also generally be a jerk, he concocts a plan with Wade to humiliate him, so that he will no longer menace the locals. Knuckles would phrase it as if this loser at a bowling alley is equivalent to a local warlord, and all is fair in love and war. But of course this would then be a character arc for Knuckles as well, as he must also learn to be a better (and more honorable) warrior. By using his power to win at bowling, the rogue GUN agents find him, leading to the episode where they capture him, which doesn't necessarily need to change (assuming we're stuck with the series really being about Wade and not Knuckles).
The GUN agents now know Wade is travelling with Knuckles, and recruit Pete (Wade's dad) to get close to Wade and kidnap Knuckles, and most of the same story can happen (even if it is a stupid story). He can kidnap Knuckles in "The Flames of Disaster" episode, and when Wade finds out it's him, he can just say he was trying to protect Wade from this alien demon thing. And even though that's obvious bullshit, Wade will believe him and simply explain that Knuckles is his friend (or sensei or whatever), and Pete can pretend to be surprised by this. Then Wade asks if maybe he's reconsidered being partners at the bowling tournament, but can give a sob story about how he's come to respect Wade, and wants to have a real one-on-one competition with him. Good sportsmanship, as a sign of respect and love. And Wade would be conflicted because he's been using Knuckles to cheat the whole time. But actually it's a moot point because his dad only says this to get him and Knuckles to let their guard down. Knuckles is of course also very naive, and this can be a parallel drawn between them. Meanwhile Pete is obviously being a dick and abandoning his son yet again.
So they get to the tournament, and Pete sells them all out, as he does in the actual series, largely so that he can eliminate Wade, his biggest competition, from the tournament. He doesn't really care about Wade, or even about sportsmanship. But what he doesn't expect is that when he calls GUN to pick up Knuckles, they show up with a giant robot, not taking any more chances. They carelessly wreck the bowling alley, and a big girder or something falls on Pete, and Wade is such a good guy that, even though he has every reason to hate the guy, he saves him. Then Wade, and maybe Pete, has to do some pivotal thing that causes the robot a moment of weakness and allows Knuckles to beat it.
Then we cut to an epilogue of Wade and his dad at the end of an extremely close bowling match, and Wade wins, and his dad shows signs of what seems like maybe sincere respect, and Wade shows signs of what might be forgiveness, but more importantly, self-respect. And then we zoom out to see that this bowling alley is in a prison, and a guard comes to grab Pete and say visiting hours are over. Wade leaves, and meets Knuckles by the gates, and Knuckles says he is proud of Wade, who now has the spirit of a warrior, and he starts talking about how Wade's relationship with his father reminds him of his own complicated relationship with his ancestors. "Let me tell you the tragic tale of the fearsome Chief Pachacamac, whose hubris led to the downfall of his people." And Wade is like "That guy? He seemed nice." "His spirit may have been calmed by the teachings of eons, but long ago..." Then music starts playing and the credits start rolling. And the theme song isn't Warrior by The Bangles, it's Damn It Feels Good to Be a Gangsta by The Gheto Boys. (Because of course I know they couldn't just play Unknown from M.E., like they obviously should have.)
So to summarize, Wade Whipple is the best member of the Chaotix, and should have been in the recent IDW Chaotix 30th Anniversary Special. Also, as Knuckles' successor as the Guardian of the Master Emerald, he is infringing upon the copyright of Lara-Su, and Ken Penders should sue.