I do hope this makes sense. I'll try and be as detailed as possible. It seems most of the conflicts that we've been waiting to be solved already are completed. Example: no more roboticized mobians, the entire Acorn family re-established (King Acorn, Prince Elias, The Queen), Annonymous revealed and destroyed, Evil Antoine, who was pretending to be the regular Antoine, of course, also revealed, etc.
I'm basically listing events / conflicts since day one in the comic series as an example. But, it seems recently that there hasn't been much of a thrill recently. You know, something that we would be having to wait for in the upcoming months. Don't get me wrong, I still enjoy the comic series, there just hasn't been much of a thrill since around ish. #169.
There have been those stories on Dr. Eggman's attack on Knothole, Sonic Vs. Tails, Enerjack's return and the destructix. Anyways, just wanted to put this in. Though, hopefully maybe we'll get a hint on what to possibly expect. I don't know, maybe it's just me.
The Bird Armada that's vaguely hinted every now and then.
So far, Bean, Jet, and Predator Hawk have stated that they fled/abandoned it in someway.
Honestly, I think that this will be brought up in issue 200. But that's just me. It's all possibly some backdrop reference from the game gear Tails' Adventure game, and we all know who's going to be the main lead. 
Even though it's Tails' Adventure and HIS story...
"It's Sonic's book," the writer says. Naturally, that's why Sonic had the spotlight fighting Knuckles' archrival.
However, it would be neat if Tails could get his own "backstory series" all to himself, spanning ten or so issues, over on Cocoa island.
And for those who have never heard of Tails' Adventures, http://en.wikipedia.org/wiki/Tails_Adventure
It was such a fun game!
Black Doom will be appearing in the comic sometime, I presume.
Eggman is still around, though that conflict has been put on hold while the Freedom Fighters deal with other villains. I am sure he will be back.
Even though I dislike when the anti-FF's appear, it could get interesting because the Freedom Fighters do have some unresolved ill feelings towards members of the anti-Freedom Fighters.
Yeah, I guess there are a few conflicts waiting to be revealed. Thanks for your responses. I appreciate them.
Personally, I see Knuckles and Dr. Finitevus becoming a new pair of arch-nemeses. Knuckles has been lacking one ever since he died, and all the other villains are taken: Eggman-Sonic, Mogul-Tails (assuming that antagonism is still in force), Shadow-Black Doom, and so on. Dr. Finitevus is the coolest Echidna villain on the block now, and after the Enerjak saga they're spoiling for a showdown. I like to think of Finitevus as the Moriarty to Knuckles' Holmes-no necessarily in them both being brilliant, but in being the veritable incarnations of good and evil destined to face off.
