Last time we touched on this issue a bit (with the characters of the game) but we'll be going beyond that for...
Part 7: The Conflict: bosses, villains, risks, threats...
First, let's divide this up a bit.
- Bosses
- Main Villains
- Risks to the World (universe, future, etc)
- Threats to the Characters
Bosses
So Color's had better robot designs, honestly. Somewhat annoying, the Eggpawns were memorable. The...things in 06 were more serious but ended up rather lame and annoying themselves. But what really counts is the actual boss fights.
06 had a couple rival battles, which are always fun. Silver's "it's no use" is infamous for it's flaws, but that fight is actually very easy. Most Sonic-fights are after a pattern is discovered--that's standard.
Iblis parts 1 and 3 were intresting. Part 2 was kind of time consuming and disappointing (it has to be done as Sonic and Shadow), but not bad. Mephiles had awesome fights, though with Omega it slows down a bit. Eggman's could be challenging, or a breeze. In all though, they were all exciting to play out. The setting, dynamic designs, and variety per character made me want to shoot for an S-rank.
Although Colors had a variety as well, they were all the same in the end: frustrating robots. They weren't any fun, and it was hard to remember which wisp-gimmick to use to help. They aren't memorable, and are very lame when compared to bosses in other games. Really only the last battle with Eggman is worth playing.
Main Villains
Yes, Eggman in Colors was probably better than his creepy 06 version, but what about Orbot and Cubot? They sucked and were an insult to any long-time Scratch&Grounder fan.
Iblis is neat in concept but he's not nearly as cool as Chaos. Solaris is confusing and a waste. But 06 also supplied us with one of the best villains in Sonic history--Mephiles. And I'd argue that his appearance outweighs Eggman's in Colors (which is alright but hard to take serious).
Mephiles is skin-crawling creepy, especially for a Sonic game. He's the cause of most of the conflict in the game, and only "craves destruction." He fools Silver, taunts Shadow, and kills Sonic. Back up, did I just write that? It's still hard to accept that's what happened. I don't really consider it since they revive Sonic with the magic powers of chaos energy and looooove, but still. Eggman's always trying to do what Mephiles did in 5 seconds!
Many find Mephiles' motives confusing. Why not unite with Iblis right-way (since he can time-travel)? Why send Silver to kill Sonic when he could do so himself? So on. But it's clear that he enjoys the suffering of others, and most fan-explanations end the same: Mephiles did what he wanted to.
Continuity thoughts aside, Mephiles' plays his main role well. He manipulates Silver and Blaze and torments Team Dark with knowledge of the future all while keeping in control.
So Colors vs 06? Colors is creamed. How can anyone take Eggman seriously with those two dumb-bots (or that dumb plot)?
Risks to the World (universe, future, etc)
In Colors, an entire race of beings were at stake. Unfortunately, I hate wisps. They were annoying and did nothing to make me like them. ScrXw Yacker, why should I care?
06 starts out with concepts that continue to grow. Soleanna is at stake. The future is at stake. TIME-SPACE is at stake. So maybe Generations would have a chance, but no, not Colors.
The past/present'future>crappy aliens
Threats to Characters
So in each game there was a physical threat to the characters involved, but that's standard. Sonic 06 gave more purpose to those involved through personal conflicts.
In 06, Silver had his moral questions--was killing someone to save the world the right thing to? Likewise there was more to Shadow's story. Mephiles tried to convince Shadow to turn against humanity, then caused tension for the team when he revealed not only Shadow's fate but a bit of Omega's. For Sonic's episode, conflict was mainly for Elise, who tried to balance her feeeeelings for Sonic (and a life of adventure) with her duty (and life in Soleanna).
Colors' kept the conflict straight forward which also dumbed it down. In contrast, 06 had layers for the different characters and storylines, making the threats all the more serious.
Conclusion
So overall the "conflict" in Colors is not serious. It does nothing to make one feel for the characters or conflicts involved. 06 was far from perfect, but it had a villain that was powerful and manipulative, it had high stakes, memorable bosses, and it added to the story instead of diluting it.