No game is perfect, I will not deny that, but Sonic 06 does have many flaws.
That said, here are some of my responses from complaints:
"The Sonic/Shadow/Silver story sucks" - Like I said, no game is perfect, but what do you exactly mean by "suck." Silver's story was good, and it instills headcanons on his backstory (such as his parents); Shadow's story was not too bad, either, in fact, it is good to see him work as a GUN agent; I have mixed feelings about Sonic's story, though (I concur on the rescue-the-princess part, since you would think Elise would try to escape all by herself once in a while).
"The title is unoriginal" - So what? The upcoming live-action film has the same title as the first game, the OVA, the Archie and IDW comics, and the 2006 game. Why don't I hear complaints about that? Also, the Transformers kept the same title in many works, as well, so what is exactly the point of this? Do people really expect franchises and merchandises to have completely different titles, or something?
"Princess Elise" - Yes, I can see your point; Elise is not a very well-developed character; she constantly gets kidnapped and has to be rescued by Sonic without trying to rescue herself once in a while, and she lacks personality and character. And besides, just because a character is a princess does not mean they are helpless, I mean, look at Sally Acorn, and even Sera from the OVA fought off a few enemies sometimes. I do wish Elise was better developed, though.
"The loading times" - It depends on what technology you have, how old it is, and how many GB's of RAM you have.
"Sonic is too tall" - What do you mean by "too tall?" Sonic is 15 years old, and Elise is taller because she is a human. This complaint might come from fans who played the very first games, in which Sonic is short, but I wouldn't know.
"Bugs/Glitches/Slowdown/Bad controls/etc." - Again, it depends on what technology you have, how old it is, and how many GB's of RAM you have. It could be your technology that causes it, and not the game itself.
"The graffics sucks" - Really? What about Sonic Adventure and Sonic Adventure 2 when they debuted in SEGA Dreamcast? Or, how about the graphics in later games, since they suck even more, especially on how they designed humans. And the promo art looks just fine; I don't see what is all the fuss about regarding graphics.
"Sonic and Elise bonding" - As friends, that is perfectly fine; nothing wrong with humans making friends with anthropomorphic [extraterrestrial] creatures. And besides, Sonic and Chris Thorndyke are friends, and I see nothing wrong with that. And many outside series like the Transformers have sentient giant Mecha robots making friends with humans (mostly Autobots), or even enemies with them (mostly Decepticons); I don't see complaints about that (except for maybe some ungrateful misanthropists). The only problem I have with humans and humanoids of different species bonding is if they are shipped as lovers (I mentioned earlier that it is bestiality, in which I do not support).
"The main villain(Mephiles)is a recolor" - Really? Mephiles The Dark is a recolor? He has two different forms: one looks like Shadow with blue instead of red (and no mouth), and the other is more brilliant in blues and purples. So, he looks like another character, so what? And why stop there? You could say Scourge is a recolor of Sonic, since they look alike, with the exception of fur color and accessories. You want to see a real recolor? Look no further than Coldsteel The Hedgehog.
"Sonic giving the young Elise a Chaos Emerald" - I don't have any refuting claims on that; this may or may not be canon...
"Cheap deaths" - Sonic X has real deaths, go check them out. And besides, American Sonic is aimed for young children, so of course deaths are cheap.
"Voice acting" - Well, you may have a point; 4Kids was not good with voices, but at least Shadow The Hedgehog and this 2006 game had better English-speaking voices than the later games starting with Sonic Free Riders. Then again, the original Japanese voice acting is better.
"Sonic dying" - Not very common to see main characters die, but I have no problem with that trope. However, there is no need to complain about death in games or franchises that originally had death in it. Have you seen the original Sonic X?
"Elise kissed Sonic" - I don't support kissing different species, I agree. But, suppose she and Sonic are the same species: it wouldn't be very common for females to give males the kiss of life like in many kids fairy tales. But, regardless of gender, I don't support kissing dead or unconscious people, because usually that would make them call "rape" because you were not given consent (and necrophilia is a sickening mental illness, so I do not support that).
Overall, the 2006 game was not too bad. I play this in Japanese with English subtitles when I am with my cousin, but I like playing Shadow The Hedgehog better, since it has a more coherent story, and you can choose to use tools along with powers (and the karma meters for Hero or Dark intents).