Plothole: Sonic and Knuckles versus Sonic Adventure

I remember reading a translated version of the Japanese Sonic 3 and Sonic and Knuckles manuals which seemed to describe a story about Knuckles' civilization, how the gods threw the island up into the sky, and that they recreated one more of his kind. Or something like that. It was kind of confusing actually. Anyway that's not really the point of this thread.
The point is, the stories correspond more when you read the original Japanese manuals, but here's the plothole. In Sonic and Knuckles, the Master Emerald is kept in the Hidden Palace Zone. In Sonic adventure, and all the following Sonic games thereafter, the Master Emerald is kept on top of a pillar out in the open. Originally it was hidden, now it's out in the open? Oh but here's the other thing that puzzles me. It's always been in that same spot for thousands of years according to Sonic Adventure, so having the Master Emerald moved throughout history doesn't seem to work either. Because in Sonic 3 and Knuckles, it's well hidden in a secret place. But in Sonic adventure it's out in the open. Perhaps they did that because it was easier to do the story that way? Still, I kind of think it would've been smarter to have the ME hidden away. Very little is mentioned about Hidden Palace, but it just seems like Knuckles' world was a lot more mysterious back in the day.
And then there's the ghosts of Sandopolis Zone, I kind of wonder if they're the lost souls that were killed by Chaos.
Not to mention the mural in the Hidden Palace Zone of Sonic fighting Eggman. Yet these don't seem to be mentioned either.
There are ghosts in SA2, like King Boom Boo, but I think he's something totally different. He's from Pumpkin Hill, which far as I know isn't part of the Floating Island.

Oh here's a link to the story in the original Japanese Manual: http://info.sonicretro.org/Sonic_the_Hedgehog_3_JP_Manual

Wow, that IS confusing. Maybe since Eggman found the Master Emerald Knuckles decided to find a new place to put it or something.

i suppose, but you cnat blame them, i mean the ycant exactly launch into a big explanation...

That's always something that's bothered me too. How hard is it to keep a story strait. A lot of my favorite video game franchises have done stuff like that. I guess it's just something we're going to have to accept. I think a lot of it is because different people work on the various stories.

At least they kept the Master Emerald part right, and the fact that the Chaos Emeralds gather around the Master Emerald. But what about the Super Emeralds? Do they just...not exist anymore?
I kind of think the Super Emeralds might've been a gimmick for the Lock-On feature of Sonic and Knuckles.
They really messed up the Archie story too. In the archie story it started out with just a chaos emerald holding the island afloat, and in archie there was at one point in time, millions of chaos emeralds located in zones. Then like 12 or so emeralds were merged into the "Master Emerald" after an epic battle between Super Sonic, Hyper Knuckles and Turbo Tails versus Master Mogul, which ended in him getting sealed inside the massive emerald. A plot which, I think was meant to result in there being a Master Emerald. But eventually Mogul would escape after Eggman broke the Emerald etc. etc.
I liked the idea that there's actually more than 7 emeralds because it makes a little more sense. I mean, if you look back at the original Sonic games, you had emeralds on South Island, Angel Island, etc. It's like each island had it's own set of Emeralds. Knuckles thought the ones Sonic had were the emeralds that belonged on the Floating Island.
The other plot hole is...how the crap did Knuckles just punch out Super Sonic?
But you can't say that the Sonic 3 plot wasn't really all that limited. I mean, there was an actual story there, and I think my favorite moments in S3&K were when Knuckles finally found out that Eggman/Robotnik was the real bad guy.
In any case, he could've moved the Emerald, but what about the scenes from the past in Sonic Adventure?
Perhaps one explanation could simply be an alternate reality. But if we see from Amy's perspective, we do see hints of past game story lines (like Sonic CD for example, there was this scene of Sonic saving Amy wasn't there?) plus Metal Sonic could be seen in a stasis tube in Sonic Adventure.
I've always tried to figure out just where in the game Sonic CD would fit in. Sonic 2 and Sonic 3 directly follow one another, so one would probably either have to believe that Sonic CD took place either after Sonic 1, or after Sonic 3 and Knuckles. Or else that was also an alternate reality, but I remember a cheat code that showed an image of Tails in Sonic CD saying something along the lines of "See you in the next game." I believe Sonic CD was created around the same time as Sonic 2 wasn't it? But I've always wondered where it fit in the storyline.
I've always kind of believed that Sonic Adventure simply picked up right after Sonic 3 and Knuckles, or even after Sonic 3D blast. I don't know if I'd consider Sonic R canon, but it did have a plot. Sonic 3D blast did have Cameos of Knuckles and Tails, who took Sonic to the special stages.
I guess it depends also on what you consider Canon and what you don't. Right now, I think '06 is the only one I don't consider canon simply because it cancels itself out and there's just way too many plot holes. The game gear games...I guess I'd consider those an alternate universe that went along with the Genesis games.

Well that may be a possibility. After all, there was never any city per say in the Genesis universe, and no humans either when you think about it. So an alternate universe is definitely a possibility.

The thing is that back then SEGA wasn't worried about plot or story or even logic for that matter. (Which explains Knux's ability to K.O. Super Sonic)

All that mattered was the one thing that made Sonic famous: Speed. I swear the Super Emeralds were created as an excuse to get Sonic to go even faster and that's all. Change the name, give him an attack, and pour on the SPEED, that was it.

Now, SEGA's too worried about plot and ignoring what it took to make good Sonic Gameplay. And now when you add that to their horrible game writers because quite honestly the Dash Adventure has a better plotline than what they come up with (shameless plug), we have a failing industry.

I think plot did play some part in the games though. Maybe not the very first Sonic the Hedgehog, but in Sonic 2 the plot started to develop some more, especially with the introduction of Tails and the Death Egg.
In Sonic 3, the Plot expanded even more with the legend of the floating island, which I always found fascinating. Sometimes I'd even stare at the clouds, and imagine one of those clouds to look like a floating island.
It also introduced Knuckles; although he wasn't playable at first he added some humor if not some annoyance into the gameplay.
I think one of the reasons I'm not crazy about Sonic 4...besides the fact that it just seems kind of monotonous that they're doing a Sonic 4 so late in the game after Sonic and Knuckles and that they seem to think going back to 2D is going to be the answer to all their problems. But the plot is also very cut and dry.
Eggman's getting revenge, Sonic says goodbye to Knuckles and Tails and goes back to running on his own. Yeah, huge plotline. It's actually kind of lame.
And like I said before, the most memorable moment for me in Sonic3 and Knuckles was when Knuckles finds out who the real bad guy is, shortly after you face off with him.
So as you can see, IMO plot is almost, if not just as important as the gameplay. It's always been there, it just may not have been jump out in your face like in recent games.
Now I havn't played a lot of the recent games, but I have played Sonic Adventure 1 and 2; I've found no problems whatsoever with the gameplay, other than some little things I nit picked over. The treasure hunts were a pain in the butt. The fishing was easy...but fishing? Really? In a Sonic game? All Tails did in SA1 was race Sonic, and I wasn't crazy about the Tornado or Egg walkers in SA2. Amy's gameplay was kind of interesting, but all she did was run away from a Robot.
But Sonic's gameplay was still good, and even more interesting with the homing attacks and the grinding made it more challenging.
I also didn't think Heroes was bad, it was just challenging to me. I don't think lack of speed and challenge was really an issue for me. Now, I haven't played a lot of the newer games so I can't really say. I'd like to though.