There needs to be procedurally generated mini bosses that show up in later game missions that can't be killed by traditional damage. Moreso, they should be able to deal high level damage to you, enough to take out end-game level frames in only a few hits.
To beat/survive these enemies in missions where they spawn you have to do something more strategic. If you fail to do these things, they kill you and you lose regardless of how many formas you have, what kinds of mods, etc.
Steve talked about how he wants the game to have more intrinsic value, and this could be a way to do that; to utilize sparse but volatile mini-bosses that completely negate the value of farming. And maybe you don't have to defeat these enemies to complete the mission, but they make it much harder, and to defeat them, you have to go out of your way.
I'd say a good start for something like this is maybe being notified that this kind of enemy is in the mission. A player less interested in combating them may then use this chance to use stealth in order to prevent alerting them, as these enemies wander.
Next, there's scanning. By scanning the enemy, maybe in a few different spots, Lotus is able to discover the enemy's weakness, if it has one. If it doesn't you will be notified, and stealth, or evasion is the only option. Otherwise, a sub-mission will begin.
These are a few ideas for how it could go down:
-You scan a quadrupedal mechanical enemy to find out that it has a charging station somewhere in the mission. While it is configured to be invulnerable to weapons and abilities not registered in the ship's systems, its shielding is vulnerable to things like explosive barrels or leaking fire. It must use excess energy to maintain shielding against this. Along with this, it must expend energy to fire a one-shot kill laser at enemies. While the laser tracks before firing, it can be dodged if you leave the area it locks onto.
The player can use any combination of forcing it to fire this weapon, or setting off local explosions to deplete it's shields. If they do this enough, it can become vulnerable, however if its shields get too low, it will attempt to return to its charging station. If it does so, it's shields will return, however if the player finds and sabotages it's charging station, then upon returning, it may either reconfigure into an ally, or be destroyed, either way leaving you to continue the mission stealthily or chaotically.
-You scan a ghoul-like mutant that constantly grows a sludge-based fatty exterior, roaming around. He is invulnerable to damage, but he is slow as long as he doesn't notice you. He has a blade for an arm that will pretty much cut through anything. He has a a gun in the other hand, that shoots a tracker onto your warframe. If it hits, and activates, he will pursue your warframe aggressively through the mission killing everything in his path, which may even cause the area to be locked down till he calms which doesn't happen till either you or him is dead. If he kills you, the tracker is destroyed as well, but there are other ways to get it off. It is only your warframe that he can track.
The player can either attempt to remove the tracker by first attempting to hack a console to force an area lockdown, while the mutant is in a different area, and then try to hack the the tracker. If they attempt this while the ghoul is in the same room, it will kill them most likely. The player could also slip into void mode dash through the mutant, and in doing so, grab an inactivated tracker. If they wanted to send the mutant on a rampage, they could dash though another enemy and pin the tracker to them, which would activate it, or dash through the mutant himself, planting the tracker deep inside him, causing him to constantly hack away at his own guts. The mutant would only be vulnerable to this if he is not alerted.
There are many different implementable combinations that would require the player to be willing to think on their feet, and beating enemies like these would hold a lot more value than just rewards. It'd be a challenge for all players, and would definitely reinforce the stealth aspects of the game. Sigils would probably be a worthy reward for killing them.
EDIT: If any of you were interested in something like this, I'd also be interested in hearing more scenario ideas.