You can try
pdftk. Maybe you have to do some scripting for the task you want to accomplish. Actually, looking at the man page you can do it on one (very long) command line, but I'd suggest to extract every single page from each pdf (giving appropriate names to the outputs) and combine them together in a single shot.
Edit: I've just found a
solution on the official site of pdftk, which builds the "very long command line" by scripting. I have not tested, yet.
merge files, given its odd and even given
