As someone working in comint I can assure you that there's nothing special about MEGA compared to others in terms of flagging.
Does that mean usage of all file lockers are equally flagged as suspicious?
My memory gets a bit patchy here, but I'm pretty sure the detective said something along the lines of "MEGA is only ever used for <thing I was accused of>". Which struck me as blatantly false and indicative of either an agenda or incompetence.
And I tend to subscribe to Hanlon's razor:
Never attribute to malice that which is adequately explained by stupidity.
I think Hyphanet or IPFS or the like with fixed and padded bandwidth links will be the next step in privacy. Again, there are consumer ISPs selling netflow data!