Initially i was submitting a paper application, but decided later to submit online.
i did not get an invite to apply online.
what i understand from this thread and others, previously you were not able to submit online. Only those invited or knew (can apply online) could. Some faced issues while submitting their applications online. The system wont let them submit.
I just went through and applied online to save time and avoid any hassles. My application submitted successfully and got an acknowledgement email. I see no reason CIC telling me to apply via paper now

i believe its easier for them also to validate online applications than paper.
Eventually CIC is starting to roll out to everyone, very soon.