A lot of the elements I think are underrated.
I see a couple of positive things as far as Elise goes... they are adding a higher level of presence for humans in a Sonic game.. a good thing... it's also a direct attack on the comics, also good. And it's also drastically playing down the furry aspect of Sonic by giving adolescent gamers something to look at besides Silver's sumptuous curves. Putting Elise as far as into the gameplay was really bold... and therefore in my book good. Sonic could conceivably carry a human and might have to to save one.. therefore a game should show him doing it. The problem was of course the way it was handled... I
thought they were going to be mini-stages with perhaps not even any jumping... for all intents and purposes, that's the way it should have been.
Mephiles is good.. he looks boss.. and he's unique as far as the Sonic world goes. It's cool to have a ghost, a "shadow" as a villain... and with that idea they did a great job imo, he is just a really cool villain with cool powers, cool entrances, and he's really detailed which is impressive.
Rouge and Omega actually are relevant to the story, much more so than Tails and Knuckles.
Silver cared about Blaze dying, what are you talking about.
Sonic06 didn't "complicate the crap out of" Rush, it retconned it. Or in other words, it's completely seperate from the Rush version of Blaze.
Silver isn't generic either. He's cute and cool, his design is clever (what with his hair that stands on its end whenever he's using his telekinesis as well as his god-like pose when flying) and his powers are totally unique.
The rest of what you said is about the Last Story and I agree with you for the most part. It should have been handled better.
Like if I can think of a better version... like, Mephiles should get an emerald in Shadow's ending, and Shadow should lose (in fact, Mephiles might as well kill him) instead of having Mephiles appear with an emerald at the start of the last story. The place where Sonic dies shouldn't be the lame adventure field recycled... it should be someplace new. An open field like in the cutscenes. And Sonic should face Mephiles instead of being killed from behind. And maybe a boss fight could happen you can play. But then Sonic dies. But Elise wouldn't scream, she'd just cry. And fire would come out. And hed be Solaris. And then it should show an alternate CG, instead of the world becoming dark, rather a more dramatic giant explosion or something and the other character reacting. THEN the shadow. Also, the last area "End of the World", it should be subtlely hinted at that it's in fact the afterlife. And the characters shouldn't be all together, just Elise, dead Sonic, and maybe 1-2 other characters. (Blaze comes to mind) and then you play as Blaze or Elise (not too late to develop Blaze! in fact that would rule) and have to go to shrines in a new adventure stage to pray to the other characters, in fact accessing each character's stage. Each character would have a full stage as well as preview cutscene of them waking up in this place and realizing they need to find an emerald. (perhaps innately knowing somehow that Sonic died) Or maybe each character takes their emerald to the next character, tells them what happens, and so on until the last character meets up with Sonic. (in other words I guess, only Shadow and Silver meet up with Elise) then Sonic is revived but the kiss should be on the forehead or cheek or something, come on. And finally the boss battle would have to be completely overhauled, it would be Solaris but there would be elements of both Iblis (fire) and Mephiles (purple/black ghostly stuff) coming from it and would have the attacks of both... and you'd fight over the burning ruins of Soleanna with a purplish sky (colorful, awesome, much more visceral backdrop than the current one)... and character swapping would happen right away in a cool warp animation via Chaos Control. And it wouldn't be a puzzle, you can attack right away with any character of your preference, or be creative, and mix it up. And Super Silver would be more dramatic, his attacks would have to look stronger, like when he flings back objects he has to move more, and when throwing them back the objects should move faster and maybe leave behind a glowing trail. Also a Blaze and Silver reunion scene would have to be added. And that's about it. Way better.
But having no story wouldn't work. It's not why we are fans.
Sonic stories are good as long as they keep being dramatic and parodical... should be driven by characters, music, and enthusiasm. They should justify the intensity and destruction of what happens in the gameplay. Rush is just half-arsed to me as far as story goes.
Going back ten steps to make a cheap (and ugly) 2D game with cheap story and 2D gameplay through cheap, unrealistic stages is not what I'm into. You can have it, and you got it, and you're getting it again, but imo Sonic really, really needs a new serious 3D title eventually... that is if Sonic is going to have a future and not gradually spiral into obsoletion, or worse, become Megaman.
I personally wish they aren't taking Sonic06 as a reason to step back from serious console entries for an indefinite period of time... that's horrible. They have the game engine and graphics all done, they can pretty much just cram out a new game and focus on the stages and make a Sonic Adventure 2 equivalent of Sonic06. (no town stages, no CG cutscenes, no loss) If they fix up the issues and
tighten up the controls in level 3 so to speak, people will notice, reviewers will notice. Make a sweet downloadable demo showcasing the changes.
Just my opinion.