"The saving system is, it is true, particular. It can be annoying."
We think it requires a bit of practice and not a short period to judge it, because once again it is inspired of what Diablo 2 did, for example.
It saves when you quit the game, when you fail, when you finish a mission, and it always saves for security.
So, you quit the game during a mission, for example. You'll resume again when you were in the mission, but physically you will be at your last deployment point.
This system has been chosen for immersion. When the player quits the game, it is as if the character returns at the base, at the temple, so it wouldn't be normal if he reconnected at the same place and time he was when he departed.