I don't think any games really have done this. Mass Effect slightly did it.
BUT, Destiny could benefit ALOT on the side of immersing the player with this idea.
We all have ships right? Ok, but what happens when you start a mission? You "teleport" to a starting location. We instead should have our ship physically land somewhere, and walk out of our ship on foot. It could be a holding area for gear and armor, weapons, our multiple speeders (unless you scrap the others).
Better than landing? Running to your ship amidst heavy gunfire, running up the landing pad, then laying one last round in a fallen Captain's skull before you take off.
Oh, you think your done yet? NOPE!
As you take off, one of your fireteam members keeps the landing pad open, and gives the enemies a parting gift in the form of a ROCKET LAUNCHER!!!!!!!
DeeJ, Bungie, MAKE IT HAPPEN!!!!!!!
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I don't think ships were designed to actually fit someone inside.