I actually found Heroes an interesting game. Though I'm with you on the whole low-quality boss encounter and the repetitive enemies. The storyline was pretty decent. SA1 was pretty much the same thing with the whole "Robotnik's convoluted plan to make Eggmanland." thing. Heroes was a different approach with the whole Metal Sonic being behind the whole thing.
thing.
Also, Shadow was a good character. If I remember correctly, Sega brought him back because the fans loved him so much. Also, E-123 was pretty badass. (Gamma was cool too, but...)
The one thing I hated about Heroes was how ridiculously long the levels were and how if you wanted to get an A-Rank, you pretty much couldn't miss a level up and you pretty much couldn't get hit at all if you wanted the ring bonus. Not to mention how just plain ridiculous the extra missions were. Like Team Dark's "defeat 100 enemies in Casino Park" thing. Which to this day I haven't bothered with. Also, it wouldn't have killed them to make the CG scenes a bit better. The artwork of those scenes was horrendous.
Bottom line, each game has it's ups and downs. Personally Sonic 06 wouldn't have been such a bad game if it weren't for the bugs and glitches. It had an epic storyline and decent gameplay.
Storyline was decent? SA1 had at least the decency of giving us an old prophecy told to us by random events and a more-or-less coherent narrative when told by several people, as well as NPCs which had their own little stories happening around them. Heroes was basically something thrown up just to put everyone together and to make them go as teams on levels. It was AWFUL.
And Shadow? Shadow was a good character back when he had a motive to be alive. He was brought back because the fans couldn't shut up about him, even though he died a fitting, hero's death. Subsequent games have him doing God knows what completely out of character. And E-123? Badass? It's just a robot who wants to kill everything. A one-dimensional character that pretty much lacks any kind of style, and it's just a bulky and evil version of a much superior character who had pretty much the only quality storyline ever told in a Sonic game (at least in concept).
And Sonic 06 is pure and simply a MISTAKE. In theory, yes, it would have been good. But the stage design, the gameplay, the levels, the graphics, the story, the... EVERYTHING is so atrocious... The gameplay just doesn't work. You get stuff like a slide which you can't get out of, you have to disable enemies to throw at other enemies in clear and stupid ways and the vehicles move badly. And the story? Human/hedgehog kissing? Shadow recolor going crazy with evil and destroying the world? Urgh... the side characters made no sense to have there, and each mission was such a complete murder of the gameplay, I felt sick.