Sorry for the Delayed post. By now Everyone would have seen the after effects of The Flash and Arrow. If you haven't please beware, as the following theory consists of many Spoilers and stuff. Also, this article has references to my previous on How Arrowverse can stay inter connected and Add some new shows to their Arsenal.
And my God! Flash did turn the Tide for the Flarrowverse. And just a small irony is, no matter how the show has progressed form the Pilot to the Finale, It began and concluded with the Flash Running against the course, quite literally. The difference is in the Pilot, he ran in the opposite direction to stop a Storm, and in the Finale, he ran in the opposite direction to stop the Singularity.
But the most significant parts of the Finale in my opinion is the Death of Eddie, The Harrison Wells and Cisco segment and Golden Age Flash Easter Egg. On observing the whole season, we can see that Cisco's new abilites are very much essential to the plot. It is like Bucky's role in Captain America: Winter Soldier. So, as per the awesome Harrison Wells, and I Qoute
I am sorry about the fact that you are able to retain traces of another timeline that you are able to see through the vibrations of the universe. It means… I wasn’t sure until just now… That night the Particle Accelerator exploded, you were affected too…Don’t be Afraid Cisco, A Great and Honorable destiny awaits you now. I only hope as you are living your great adventure, you remember who gave you that life. And that it was given out of love.
Now that's a different ability. Also this can be taken as a confirmation to a fact that it was an Alternate timeline where Cisco finds out about Harrison Wells, evidently conforming the existance of Alternate Timelines. So, Many have been questioning the possibility of connecting Flarrow-verse and Supergirl based on the Leaked Pilot.
Let's explore the different changes these reveals can hold on this universe.
If we see his abilites as per the show, he can look through the vibrations of the universe, which technically means that he is the map for the multiverse. Now, as per the finale we saw that he can feel traces of the other timeline he was through even before getting his powers. So let's assume that his ability when fully activated, it will definitely include an ability to phase to alternate timeline.
Now, As per we know about him, during the Flash of Two Worlds events, we saw that Barry and Jay did had some adventures together and for Barry, Jay was just a comic book hero who turned out to be real in an alternate timeline. This also answered many continuity clashes which were creating trouble before this event happened. By the end, we saw that these different timelines merged together to form a single one. That's how we got a new universe with lesser continuity issues.
Now I may not be accurate over her, but as per the leaked pilot, the Supergirl universe has Superman around for a long time (approximately 10 years). So, it's tough to have the Flarrowverse and Supergirl universe to be connect before the Flash Season finale. But now that Flash's status quo is completely altered and literally anything can happen. So, in this suitation, imagine that Supergirl takes the place of Jay Garrick. Then there poses a possibility of their universes combining at a later stage like the season finale of Supergirl.
How can this happen?
For this to happen, all we need is just an Episode in Flash season, around the Mid Season finale dedicated only for the Alternate timelines. Then in the Season finale, Barry get's an unknown help from a mysterious person who turns out to be Supergirl. They are suprised by each other and start to fight it out only to sort it out later by the season end. That's when we see multiple timelines colliding with each causing ruptions in the time stream. And by the end of the episode, we get to see a new universe in which things are running differently. Where the Flarrowverse and Supergirl-verse are merged. So does new villans enter this world. The highlight is that only Barry and VIBE have the memories of the previous universe. Although for this to happen, things in the Newspaper must be clarified first.
Bonus fact: Integrating the Cinematic Universe
This also can open a way to finally get the Cinematic universe to merge with the Television universe. Although that's a little different motive and meathod to implement.
With this, we saw the Cue cards the Flarrowverse have which, although can be used only once, can have adverse effects and make the universe more awesome than ever, change the way this universe operates.