While it is interesting for a RPG I feel that Sega kinda had the syndrome of turning Sonic into a JRPG with shonen elements where the stakes are getting higher and higher to the point where it's mostly about Sonic fighting a monster of the week with the Chaos Emeralds used at the last moment.
We've had that for Sonic Adventure, Adventure 2, Heroes, Shadow (for him instead of Sonic but still), 2006 and finally this one.
Sonic Colours felt like a big breath of fresh air after Robotnik got betrayed again by a monster of the week (although the DS version had a Super Sonic final boss but it's exclusively a post-game like the other Rush and Advance games).
Generations brought it back but thankfully they didn't make the mistake of having the big monster betray them.
Now the thing is that even against Perfect Chaos the Emeralds became black like in the game, is this related or just a nod? Chaos Emeralds are never "out of juice", they were probably just corrupted by Dark Gaia.
I felt that Unleashed soft rebooted the franchise by removing the G.U.N and only having Tails and Amy while for the first time ever Knuckles wasn't shown since his introductory game Sonic 3.
I didn't like Colours much because it was more humorous and too jokey. I don't want Sonic to be angsty and dark mind you, but as you mentioned for Adventure 1 and 2 and Heroes and '06 I want my Sonic games to be, like you said, a serious shounen JRPG. So what we got in those games were a-okay with me.
It's like how I never saw Resident Evil as survival horror but moreso action horror, so when everyone dunked on RE6 for getting too Michael Bay action-y I was like wtf u talkin 'bout? RE was ALWAYS about over-the-top action and cheesy one liners, RE6 just crancked it all up to 11. In my eyes that game was a natural evolution/climax of everything the whole series had built up to. But then 7 just had to ruin my fun and "go back to the roots" of being a "horror" game.
That generally seems to be a thing with me. If I like a series, I seem to like it for WAY different reasons than everyone else, and then get annoyed when that thing gets taken away because of outcry.
Resident Evil: I liked it for its action = action gets taken away.
Sonic: I liked it for its shounen tropes = shounen tropes get taken away in favor of humor and slapstick.
Zelda: I liked it for its dungeons, to hell with exploration, that was just a means for me to get from point A to B = traditional dungeons get taken away in favor of a game that focuses solely on exploration. Am I just not allowed to like anything?
Back on topic: Right, I forgot that Perfect Chaos blackened the emeralds too. Thing is, in that game it is explained that they lost their glow for a hot minute because Chaos drained them of their negative energy. They then spring back to life when Sonic uses the positive energi. But in Unleashed Sonic travels the globe to recharge them.