I've just beaten Athena too. Want to throw a few things out there.
- Checkpoint spacing is important.
- Enemies should have some semblence of a reaction time between detecting a player and taking action. Crouching slowly through a doorway and getting plugged with burst fire the instant I edge out from cover is bad. Especially in a "stealth section" (which shall be defined by a complete lack of ranged weapons available to the player). Bonus points for simulating common player limitations like finite turning speed.
- Enemies should not have randomized "critical"/"head shot" attacks. If I lose two and a half blocks of health within half a second of exposure to an arbitrarily lucky spider drone, instead of a half block or so, I don't say "wow, this game is challenging in the good way". I reload from the last checkpoint.
- Don't have infinitely respawning enemies.
- Don't have infinitely respawning enemies that don't drop ammo.
- Don't have infinitely respawning enemies that don't drop ammo in a fucking stealth section.
- Don't have infinitely respawning enemies that don't drop ammo in a fucking stealth section and throw infinitely respawning rail turrets (w/ search lights) on top.
- Avoiding object intersections during animation is a noble goal, but don't ever let it interfere with gameplay. If I try to fire my gun into the face of an enemy, a shot should always go off, no matter if the firing animation "fits" between me and the enemy. The way EfBB handles this is particularly annoying in case of the minigun, as its rev-up can be interrupted by an enemy (or by crossing through a doorway in certain ways), and then you'll have to wait another two seconds before you can fire again. BAD.
- Stealth indicators (blue tint) should be reliable. If noise/proximity/whatever is a factor in how likely I am to be detected, show it. Don't lie to me with a full blue tint while an enemy is already engaging me.
- Don't bait and switch on stealth. There are many spots in EfBB where you can approach an enemy from behind crouched and as quietly as you want, but they'll magically turn around and shoot you in the face before you can get close enough to do a stealth kill. If you want to prevent stealth kills of specific enemies on purpose, turn them around so that the player can tell beforehand.
- If you want me to solve a stealth section by exploiting enemy patterns, make sure enemies settle back into that pattern after I've upset them.
- Make sure to give me feedback about the current alertness of enemies.
- Avoid arbitrarily locking doors in a game with non-linear segments and side quests. If I have stuff left to do in an area, I need to know about points of no return so I can avoid them until I'm done.