To be entirely honest... I hadn't thought of a win condition. The problem with having a win condition is that so many of the people who would be interested in playing the "exploration" gametype would want to explore at their own pace, and may even want to look into things that weren't included as part of the scanning functionality. So if they're playing, they want to go look at an interesting shape in a rock over there, and along the way they scan the last unscanned subject in the game, it would be frustrating if the game pulled them back out to the menu. So if there is a win condition, it would have to be indicated by a UI effect, but not stop gameplay. Kind of like in From Dust where you could populate all the pillars and unlock the ability to move on to the next level, but you had to actively go through the passage to the next area.

Perhaps each base could either be built upon a Forerunner teleportation terminal (or you unlock the area containing it as you progress) that you have to activate, or the ultimate goal of each base would be to construct a human-made teleportation terminal that warps you to the next area/level. The base construction drone would build that last, based on the scans you collect.

For replayability, maybe the teleporter unlocks at 50% completion? That way you're encouraged to go back and get that 100% on every level.