I'm extremely happy they are keeping them separate. Stephen Amell and Grant Gustin are not good enough actors to be in a movie. Gustin is too young to be part of the movie, everyone in the cast would make him look like a little kid except Eisenburg. Actors in their teens and early 20's are OK for TV characters (there are exceptions of course) but I want to see adults in the big screen versions. Actors in their later 20's and above have had more time to work on the craft of acting (there are exceptions of course Gadot for example) and most of the time the lesser talented actors get weeded out in the casting process when it comes to movies. If they were to put Amell and Gustin in an audition for the movie they would very likely not make the cut. Stephen Amell isn't even the best actor on his own show, Manu Bennett is, and you want him to be Green Arrow in the movie version instead of someone with better acting skills just because he's been the character for a couple seasons on a TV show?
They are decent TV shows, well Arrow is, Flash isn't far enough in to know yet but they don't and won't stand up to the scrutiny of the big screen. The actors and storylines are fine for TV shows but movies are just better crafted in every way, assuming it's in the right hands. Bigger budget, better actors and the majority of the time better directors, better writers.
There are already several versions of these characters out there for people to digest and it's been working out fine (comics, cartoons, animated movies, big budget films). I have a hard time believing anyone is going to go into the Justice League movie and say "I don't like this because Grant Gustin is my Flash". Because when the movie is over, you can just go back to watching Amell and Gustin on TV. I think most people are capable of differentiating between the two, only people who are fixated on Amell and Gustin will really care, because they want their guy in the movie. Because odds are very likely that the movie version actors will be significantly better actors.
On top of that, once you connect the movie versions with the TV version, then that limits what the TV show can do from a direction standpoint. You might have to break off a storyline from the show for an episode or possibly more to explain details from the movie, or continue a storyline from the movie. On top of that, you have two different directors, with different ideas and different motivations for the character trying to find a way to co-exist with each other. That's not the ideal setting to make the characters and the universe function on all cylinders. S.H.I.E.L.D. is held back because of being connected to the movies, it weakens the product overall because the actors and characters in the show aren't as good as the movie versions, the main characters play virtually no role in the TV show outside of minor cameo's and budget is much smaller so the show and movie aren't on a level playing field. Then, when a movie comes out they have to write that into the show to fill in blanks, explain details, continue storylines etc., all while not having some of the most important people in those storylines on the show. Makes the TV show feel even less significant IMO.
Keep them separate, people who want the TV show connected will just have to learn to like both versions. As long as both versions are done well, I'll be happy watching both.