Honestly, it did seem like it was a combination of not enough time put in some of the projects or consideration of ideas. I never grew up with SEGA consoles and my first introduction to the Sonic games was
Sonic Adventure 2: Battle and the GBA games. So I do not know how well my opinions would work here, so here is what I think with what could be done:
Sonic Heroes: Cut the length of the stage levels. I remember that they'd often take a fair bit of time and well, you are playing as multiple characters so I get everyone usage there, but oof, the stages can feel like a chore. Preferably, make up the lost time with one or two exta levels. I understand that would probably take more time, but well, try to simplify it to not make it as much of a burden. Beyond that... it's a solid game I think.
Shadow the Hedgehog: Honestly, this game is pretty so-so. While slightly convoluted, I don't think it was that bad in consideration in giving Shadow his own game. That said, this game probably did take alot of time away from what could've gone for Sonic 06. So honestly, shelving this game for the time being would work best for the franchise as a whole. Though that said, given how Sonic 06 is perceived, it's unsure if it will break out of the limbo.
Sonic & the Secret Rings: Like Shadow the Hedgehog, shelve it for the time being. If we want to make Sonic 06 the best game, we need all hands on deck for it. I don't think should be a difficult decision. Besides it being shelved, I don't think it needs much else.
Sonic 06/Sonic Revoluton: Keep Yuji Naka to try to keep the game consistent and have this be his final game for SEGA. With Shadow and Secret Rings shelved for the time being, this could spare more developers and time to make the game good and keep it in time for the 15th anniversary release. Now, how much this would change the game... I don't know. The extra time and manpower could definitely scrub most if not all the bugs. Additionally, they may be able to give the characters more dynamic posing and animation in cutscenes so they don't come off as stiff, which is something I think would be brought up. Alternately, I am thinking some of the design choices of the shelved games would play in. Like using the models already made in say
Shadow the Hedgehog and so on if they made it that far in development. Heck, Shadow's sections may be more like the gunplay of his would-be game rather than just the vehicles here.
Now, we can be fairly certain most of the bugs would be scrubbed and likely also that the animations and expressions (including voice acting) would be alot livier. But the game would still not be perfect. Given how they were trying to go for a "realistic" vibe based on how
Batman Begins was doing and capturing that epic feel, we'd still have the story all over the place. A convoluted and strange messy story. Shadow's story would likely be simplified since
Shadow the Hedgehog is shelved and maybe it was answered that Mephiles was the one who saved Shadow for his own ends? Blaze's inclusion may or may not happen, though she could be replaced by say Cream.
Ultimately, with two games being shelved yet having enough assets that could be used, this should allow for the game to be finished on time for the 15th anniversary. Especially since the team would not be split up. Of course, there is the danger of time so SEGA may have to bite the bullet and do a Sweet 16th anniversary, but I don't think that'd be necessary if Secret Rings and Shadow are both shelved and thus could lead to a release on the Wii.
Overall, the game would be alot better in mechanics, but still be this strange hallmark storywise. It would likely be a financial success while perhaps being like a 7/10 or 8/10. Naka's departure would still leave the series in trying to move forward and the story being messy (if not as much as OTL) would reflect on that along with tone.
Sonic Unleashed/Sonic World Adventure: Sonic Unleashed was defined by the troubles of 06 and here it'd be no different. That said, 06 not being rushed would mean they likely wouldn't be as drastic in some of the changes. Given how Tails would be included, I would predict that game would go and focus as Sonic and Tails as the playable characters and stick with its original title of
Sonic World Adventure. That said, they may still wanna seperate it from the
Adventure games, but still keep the
World aspect. So could be like
Sonic World Quest or something among those lines.
So replace the Werehog stages with stages over for Tails. Perhaps borrow a couple elements from Sonic Adventure 2 and have him blast stuff, just with the arm cannon from Sonic Battle. Besides that... I think the game would be able to do pretty well for itself honestly there. A back to basics approach of Sonic and Tails stopping Eggman's scheme. Could keep the Light/Dark Gaia stuff, if just tweaked to note the lack of Werehog.
Sonic Colors: I don't see much changes here except over for expanding gameplay to include options for Tails with his differing usage of the Wisps or perhaps it'd be Sonic and Tails together. It would probably be the most alike as OTL and allow for alot of fun.
Sonic Generations: Honestly, I could see it to where it is Modern Sonic + Tails and Classic Sonic + Tails. It would sitll be a fun celeberation of the past and present over with everyone involved. That said, with less troubles from Sonic 06, I would see this being the turning point over with fans now wanting to see characters like Knuckles and Amy along with the others become playable again, especially seeing everyone here.
After this... I'm kinda at a loss on how things would go. We may still get Sonic and the Black Knight later than OTL if Secret Rings comes out still, if just later.
Sonic Lost World would potentially be pretty different. The team would have more incentive to change things and be innovative, so likely see Knuckles and Amy return. We would also likely see the desire for the
Mario Galaxy styled sort of gameplay. However, it's a matter of time and effort since the game was mixed there (from what I read, the parkour on the Wii U was kind of a mess, but the 3DS handled it better). Honestly, I could see the game being still pretty mid, but not as much. It'd be one of those games that would get a remasteriing over for the Switch and do alot better there. Hell, I could see
Sonic Lost World Ultimate lets call it include Knuckles and Amy if it didn't for the original Wii U version, thus redeeming the game even more.
Sonic Forces would probably bring more of the supporting cast to play with like Shadow, Rouge, Omega and so on over if they can find the best way to do so. I don't think it'd be difficult though. Additionally, since 06 was not a dumpster fire, Sonic Team wouldn't feel like they have to include the Wisps every so often and that would change up game stuff here.
I would think by this point we would definitely see Knuckles return here if not in
Lost World along with alot of the other playable characters. The details I don't know how it would go, but they may take elements from
Sonic Heroes or the
Adventure games and try to refine them. Perhaps a pair system? But probably no Wisps or Classic Sonic, so it would definitely see the foray of everyone there. Likely a different story to a degree since the Phantom Ruby wouldn't need to connect with Forces.
One idea could be the six teams idea they wanted to do with
Sonic Heroes (as stated by
@MegaToon1234 ) and with
Heroes potentially being here than OTL, would be fun to expand on the idea with more power and more characters. We could see the return of Fang, Bark and Bean there, perhaps as a team of bounty hunters/rivals to the Chaotix as a 5th team. For a 6th team, well we have Mighty and Ray there, but unsure who could fill in the void. Granted, if we wanted to go full retro, then maybe modernize Honey the Cat, which would fit really well for the retro vibe. Honestly, we could have a 7th team as DLC of Blaze, Silver and another outsider (maybe Shade the Echinda if things did not end up so messily there with
Sonic Chronicles).
As for spin-offs... harder to say. Sonic the Hedgehog 4 may likely still be troublesome if made, the team may not be as pressured to make it. We may still get
Sonic Mania out of the desire for a bunch of the older characters to come back and the desire for more characters there could lead to something with Amy included there along with Mighty and Ray. And then there are things off the wall like
Sonic Chronicles.