Why Not? Because they were saving Thanos for the 3rd and 4th Avengers films and chose Civil War to be one of the factors towards explaining how they'd lose. See, this hypocrisy gets annoying. First it's all "Why didn't the other characters show up in Iron Man 3 or Thor Dark World?" and then they incorporate other characters into Cap 3 and we get this attitude. Hydra was expanded to no longer just be a Captain America villain. Having him only be fighting them in his movies is lazy writing anyways.