GoPro Studio handles time-lapse nicely. Just import the folder, it recognizes each separate time-lapse based on GoPros number system and creates the appropriate grouping. Then use the advance setting to size, proportion, elimination of fisheye, frame rate and quality. Set your in and out points and click convert. Not sure how the quality of the end result compares to other software applications, but it works easily.
For video, GoPro studio works easily too and it's FREE. I have FCPX and still use GoPro Studio every so often.
Yes, since "Mavericks" Macs handle MOV files "funny" seems to convert them for some reason. Personally, I've been using QuickTime Pro the paid version. I just drag anything that GoPro makes onto the QuickTime Pro (QuickTime Player 7) icon and it plays it. It also can make movies of time-lapse still photos, rapidly too. I often use it to experiment with different frame rates since it makes the movies so fast.
A side note: I practice a bit of voodoo with my GoPros. I never plug them directly into a computer. The memory card is removed and placed in a card reader or into an adapter and then placed into the laptop and files moved to the internal hard drive or an external. I don't want the computer "telling" my GoPro anything that may lead to a freeze up of the GoPro at some inopportune time. Voodoo, like I said.