There were many unanswered questions in Season 1 of "The Flash".
For starters we don't know whether are we going to see Cisco as "Vibe" and if Eobard Thawne is removed from history how Barry still have its powers, how his dad was still in the prison, how captain cold still posses that gun and to top it off where is Barry's mom.
The answer is very simple "the occurrence of singularity". Since The Reverse bought so many changes in present and past; eradicating him from being born not only started changing past but also present and future, this lead to clash of alternate timelines which resulted in "TIME BOOM" leading to growth of the singularity absorbing everything.
Since Barry ran into the black hole no doubt he's gonna enter an alternate timeline.
So here are my predictions of what we may see in Season 2
Remember the helmet we saw in the last episode of Flash Season 1.
Well we're definitely gonna see Golden Age Flash..!!!
If we're gonna see him definitely we're gonna see Barry learning new way to use his speed.
Remember a kid named Wally West who used to live in Keystone city too.
Then for sure if we are going to see Jay we are definitely going to see Wally but as Wally not as Kid Flash for a while.
There would be no doubt that if we're going to see Jay we are going to see his arch nemesis "Velocity 9" aka "Dr. Edward Clariss"
Talking about arch nemesis don't forget Eobard Thwane aka "The Reverse Flash"
but I believe he may be called as "Professor Zoom" in this alternate universe.
We may also see team up of him with Reverse Flash of Golden Age aka Velocity 9.
There's a very definite chance that Iris and Barry were never friends as kids.
They probably meet each other somewhere else and fall in love with each other.
Remember this image?
There is a possibility that instead of Firestorm we may see Killer Frost.
That means instead of Ronnie getting affected by Particle accelerated explosion Caitlin does, which makes her one of the mad meta-humans faced by Flash.
Remember Wells saying that he was affected too by the explosion.
Well in this alternate universe he does get affected by particle accelerator and becomes "The Vibe"
We may get to watch an epic battle between him and our Flash.
Remember our power packed Meta-ape, there's a definite chance of seeing him but this time he will be seen living in his own secret society fighting for his own throne, just the way it was in animated series.
Remember General Eiling, well his most favorite and success full project was "Captain Atom". So there is a maximum chance of seeing Captain Atom in action.!
There is a chance that Barry and Jay run at speed of Mach 2 and open the portal to Earth Prime so that Barry can right his wrongs and can save its Planet.
That's all I speculate of may taking place in Season 2 if you have any idea do tell me. :)