-So when the container with Fitz/Simmons dropped out of the plane from a relatively low altitude, should it have skipped along the surface or contained some sort of forward momentum from the speed of the plane?
Some, but that thing is clearly heavy and has all the aerodynamic characteristics of...well a metal cube. The drag alone should cancel out most of the lateral inertia before it hit the water. Either way, it's got to be a rough ride for Fitz & Simmons unless they somehow managed to strap themselves down in the two and a half seconds they were airborne.
Realistically there should be broken bones and concussions at best...but this is a TV show with killer cyborgs juicing on alien bio-matter, so we can let realism slide in favour of drama every once in a while.
The way I remember it The Bus was in VTOL mode with its engines rotated so it should have been moving at helicopter speed and not a C-17s cruising speed making the splash even more survivable.