Eventually that ended, and I stopped trying to stealth. Fighting the enemy carries no penalty. So all the orders mean dick and it's just like any other MGS game, except the soldier supply is unending until you're hidden again. I am not impressed with this supposed best of the series.
It does effect the game, but not too much if your quick about it. For instance...
- If the enemy sees footprints, they'll follow them. Often right to you.
- If there are no enemies in an area for a certain period of time (because you killed/tranqed/KOed them), Command notices the lack of reports and sends in a team and activates a Caution mode. If they find a dead guy, this'll trigger an Alert mode, but if it's just a sleeping guy, they'll just wake him up.
- If you are spotted in a Caution Mode, it'll trigger an Alert mode. If they report in,
they will send in heavily armed SWAT teams or worse. This can range from guys with shields (which makes them hard to shoot), guys with shotguns (which will destroy you), or even a helicopter that will ruin your shit.
In other words, triggering Alerts means the game becomes much harder than it needs to be. You can tranq guys all day long (which IS stupid) but the second you start putting bullets in guys, your day is ruined. However, you can make Alert phases alittle easier to deal with by blowing up any ammo stockpiles you see (wooden huts with bullets/guns). This makes the enemy ration their ammo and no one unit will carry more than a single clip of their main weapon or 2-3 of pistol clips. You can also blow up the helicopter early on to keep them from sending it after you on alert phases.
Killing guys also makes one of the later boss fights MUCH harder.
One last thing: The number of Alert phases you trigger and how many people you kill dramatically effect what your rank/codename is when you beat the game. I believe this can prevent you from getting certain rewards if your rank is too low.