I like the sentiment. Gives it an X-Com vibe. Similar to your suggestions:
1) I think there should be greater consequence to guard alerts. For example, the higher the alert, the more damage you take. It wouldn't be hard to find an in-fiction way to explain this. It would something like the star system in GTA, but instead of more troops, you'd take more damage. It gives the guns blazing approach a more pronounced risk-reward balance.
2) I like your idea of character exhaustion and recovery times. This would be more like X-Com and the much more consequential use of teams in that game.
3) The item unlocks and loadouts are really clunky and unnecessarily complex. Linking that stuff to your MB staff adds too many layers. I think the MB part of the game should be totally divorced from what you do in missions. Keep it simple, effective, challenging, and fun. The MB-development stuff is just one massive mess that keeps me from having fun. It's not hard. It's just tedious. They really needed people with more strategy game experience doing this. Firaxis and others have this down to a science. This MB-development part of the game just feels like it should have been cut from the game entirely.
4) Dying should be easier (see idea 1 above). But to offset that, they could introduce yet another idea borrowed from FC2 and use buddies or MB staff to revive you under certain conditions. Say, if you rescue a prisoner in a mission, that means you get one rescue (like an extra life). That in turn, would take away from your total rewards at the mission end, but it wouldn't be a complete restart and would still pose a greater challenge at the same time.
Just a few ideas. This is a game that seriously needed someone above Kojima saying "No!" from time to time. Konami gave him too much freedom, and it ended up biting both them and Kojima in the ass in the end.