Well I think its a different timeline, a different Earth IIRC, especially considering what the movies have already done. The Civil War includes actions from Shaw (dead since First Class) and takes the House of M storyline. Way too much to cram into a single movie.
Also, these storylines rely on the Avengers and even spidey. So Im sure there are issues of getting those rights and having a cast ($$$) of a dozen plus characters some of which are worth a few hundred million at the box office alone.
We'll just have to see what they do with it. After the Last Stand, everyone was coached to say "the X-Men trilogy, its over we are going separate ways" but if you recall, I said they would be back because this is their bank roll.
One important thing to pay attention to is Magneto being with Xavier in Days of Future Past. If the next film is a Civil War or House of M story he has to turn on the XMen. Onlyin film 1 and 3 did you really see mutant on mutant struggles. Brotherhood vs XMen.