Ok so instagram's Hyperlapse is not the same tech as Microsoft research's hyperLapse, but its free, and pretty cool.
What you are really getting out of the app is a somewhat steadied and smoothed out version of your video with the option to "time lapse it" but really this is more just speeding the footage up. A big difference here is that the MS research will actually take out fast turns and bumps and look for a smoother path to follow. You don't get that with the instagram app, so any quick moves and changes are glaring . But hey, this app is free.. so you get what you get.
The most obvious difference from the start is that the output from the hyperlapse app is significantly reduced in size and quality.
The other thing is that the app seems to lock the exposure so you will not get good balance between darks and lights. I couldn't tell if there is an added filter to any of my videos. I don't think there is, I think it's just a result of the lock.
I did find though that footage I shot on my bike handlebars , which is normally super jittery , was actually smoothed out pretty well.
I filmed this kitesurfer this morning to see what some of the differences might be..
For this clip I scaled down the "hand held" footage to match size and put them side by side.
I have an iphone4s so the native video size is 1920 X 1080 the instagram app scales the video down to 1280 X 720.