In a recently leaked e-mail it was revealed that Marvel and Sony met to discuss the possibility of Spider-Man appearing in the Civil War movie. According to reports it was marvel who approached Sony with the idea but Sony pulled out.
On the exact reasons reasons for Sony to do this I can only speculate, but I think that perhaps this is slightly short-sighted on Sony's part. Since the realease of Amazing Spider-Man 2, the franchise has been flagging. Sony's attempts to generate interest in the franchise by suggesting several spin-off movies including the Sinister Six has quite frankly fallen on deaf ears. To my mind this is not really surprising, how can you have a movie based on Villans in the Spidey universe, with no appearance of Spider-Man. It doesn't really make a lot of sense, in the same way a May Parker movie wouldn't work. The fan's would love to see the Spidey go up against the Sinister Six, it requires considerable investment not just in money but also in time. These are investments that Sony seem to be unwilling to make.
Looking at things from the Sony perspective, I can actually understand their reticence. The original Civil-War story line had Spidey publicly unmask. This act alone would draw Spider-Man deeper into the MCU. Sony who wish to keep creative control of the character would have difficulty developing further story-lines with out having to further consult with Marvel, losing them the creative control they are desperately clinging too. Even without the public unmasking it would be difficult to produce a story-line following events in Civil War without referencing them in some way. This again draws Spidey into the MCU and Sony sacrifices creative control of the character.
Sony would benefit massively by including Spider-Man in the MCU, it would generate a massive amount of renewed interest in the character and the franchise as a whole and open the door for more characters crossing over from the MCU to Sony Movies. Anybody else want to see Spider-Man Vs The Hulk?
Personally I would love to see all the rights that were sold by Marvel being returned home, it seems to me that the MCU is the only production house capable of producing faithful adaptations of their comics. Which is as it should be. Neither Fox nor Sony have been able to produce a movie based on one of Marvels characters that stood toe to toe with any of the MCU productions. It is with this in mind that I look forward to the day that the MCU regains full control of all it's characters and we get to see the X-Men, Fantastic 4 and Spider-Man stand shoulder to shoulder with The Avengers.