I think it means a percentage of what actually is in the Ground Zeroes release. (I think I saw someone on Steam with a 95% completion and they were asking what was left to do to get to 100%)
Some of the things to pursue for me wouldn't be something I'd want to do.(Like trying to get the fastest speed record for tagging all enemies on the map) That kind of thing has never appealed to me.
I will be replaying the Ground Zeroes mission on the "Hard" difficulty setting though. There's the side mission I described above, another mission requiring all AAA sites to be destroyed(using C4 one at a time from a distance is AWESOME), another side mission which I found very entertaining where you have to dispatch two shady Vietnam War snipers, the Deja Vu mission which you unlock by finding all XOF patches(I used an online guide to find them all. You can alt tab out of game quite easily to read guide), there's another side mission to destroy biobot guys, and another side mission which I posted here from my PS4 experience which was also cool because it had you know who in it.
There's different cassette tapes to be found as well. I'm not sure on the specifics though as how to achieve 100%. Mainly its only the missions and any story related content that interests me.
Another challenge would be to disable the last chance shot or whatever its called option in the game. Basically if you aren't paying attention and get to close to an enemies line of site or drop down in front of someone you did not know was there(I've accidentally done that before) the sound goes tense and the game goes slo-mo to allow you one chance and one chance only to quiet and enemy before the alarm goes off. I kind of like having it on at least while I'm learning the base. But that certainly adds a level of realism and difficulty because you have to pay attention to your surroundings. Taking that option off plus playing on Hard should be interesting. I'll let you all know how that plays out and if it does so any differently when I give that kind of play through a shot.
You can also set what music plays when you call your chopper to come pick up your "acquired" personnel or when you leave.
BTW, I'm using a console controller to play this game. I enjoyed the PS4 controller very much and for me there's no other way to play it as its just too ergonomic and comfortable. I'm using an Xbox 360 controller and it works like a charm. I just use its default gamepad binding save for inverting the Y-axis. For example the right bumper brings up your binocs. The thumbstick zooms at different levels but just the other day(another detail, albeit a small one but still useful and a pleasant surprise) the up and down on the d-pad performs a gradual zoom in and zoom out for the binocs.
Here's the XOF patch location guide I used.
http://www.ign.com/wikis/metal-gear-solid-5-ground-zeroes/X.O.F._Patches
