For me it was basically that every encounter should have been multiplied by three. Those little checkpoints being two soldiers aren't worth it, and it's the same up the line. Even the big stuff almost always feels empty.
Sniper Elite 4 and 5 are comparable in terms of stealth mechanic quality, but their bases are actually filled in and they're better games for it. MGS5 could have been that, and I'm pretty sure Kojima wanted it to be that, but they pulled the plug and shipped a partial game instead.