Indeed and agreed. It will be interesting to see how they handle Barry Allen in the Flash/GL film.
The other problem you guys are getting into is creative control. If The Arrowverse and Movieverse are the same, then that means Goyer has to have Slade be a product of the island, with Billy Wintergreen a peer, and Slade has to have an obsession with Ollie Queen, and have lost the Mirakuru, and it has to be Mirakuru, and can't tie into something toatally different that they're doing. Goyer and Snyder can't just use Deathstroke however they want, because they have to adhere to Berlanti's creative decisions.
This also goes for world-spanning problems. The Movieverse can't tell a story where metahumans come from X, because Flash already established the Molecular Accelerator incident bringing all these X elements into the universe. Oh, and what if the movies want to do a storyline where Parademons or White Martians invade the whole world killing a bunch of folk... well, now Arrow and Flash have to show or at least talk about that, even if it doesn't fit their storyline.
This is on top of the Movieverse might just want to have different (better?) actors as Flash and Green Arrow, and may not work well or market well with Armell and Gustin... or maybe the Arrowverse may want to have Green Lantern guest star, but can't pay the fees for an appearance by Josh Hartnett or whoever.
Marvel gets around this by giving full control of everything to Feige and giving strict guidelines to everyone in that universe what they can and cannot do. Agents of SHIELD gets a very limited stretch of things to play with and then they get told 'hey, here's what's going on with the universe, so you have to do this storyline now.'
I wouldn't want that for Arrow or Flash. It's better for them especially if they stay independent father than having Goyer and Snyder come and tell Berlanti what they can and can't do since they only have 4 million viewers and are only pulling in so much money.