I think a big part of the problem lies with how binary the stealth mechanic is right now. A concealed Covert/Ghostwalker/SMG Shinobi can practically pin a 'Kick Me' sign on Advent's back without being noticed, but if an enemy spots an unconcealed
civilian VIP for even a split second at the extreme edge of sight range they immediately break out the micromissiles and heavy machineguns and the whole map turns into the OK Corral at high noon. It's not just that pure stealth is too low-risk - although it probably is -
breaking concealment is also too big a risk for anything but a full-size A-team, because the way the yellow-alert and pod activation mechanics combine means that there's no reliable way to engage
anything without being forced to engage
everything.
One key thing to note is that this primarily matters for hybrid squads, not those that go all in on one tactic. Solo/duo full-stealth squads don't need to worry about combat at all; they can just moonwalk past everything in concealment and then drop a one-turn evac flare and get out literally without a shot being fired. Going to the other extreme doesn't have the same mission-trivialising effect, but does still fundamentally work: a 8-10 man full-combat squad has the firepower to burn down pods as they come in without being overwhelmed, so kicking the hornet's nest becomes survivable.
On the other hand, attempts at a hybrid squad run into serious anti-synergy problems. A low- to mid-rank shinobi/specialist/ranger/assault squad is more-or-less doomed to half its members being dead-weight; for as long as the squad is in concealment the ranger and assault are non-entities; if they go loud the shinobi and specialist drag the total firepower down too much to fight through any real opposition; and there's no tools for combining the two approaches.
It seems to me that the game needs more ways for X-COM to actually
interact with the enemy and/or the environment
without subsequently having to fight everything on the map, so missions aren't forced to the extremes of kill everything/kill nothing.
My suggestion:
1) Break up the schedules into larger numbers of smaller pods. For a pure-stealth approach, there's almost no difference between an eight-man rainbow pod and a solo drone - they're both effectively just a 5-10 tile radius red zone that you have to stay out of. Go loud, however, and one is a
lot easier to kill than the other. Keep the same total number of enemies and split them into more pods, and you shift the balance of difficulty in favour of combat. (With points 2 and 3, it might even make sense to increase total enemy numbers as well - that would have to be playtested.)
2) Increase the detection radius on enemies in yellow- or red-alert. This probably wouldn't have that big an effect on its own - and in fact is almost completely irrelevant to the pure-stealth tactics that are the biggest issue - but it makes thematic sense and I think it's an important balancing factor to allow us to:
3) Add an additional ability to all soldiers that allows them to re-enter concealment if there are no enemies on the map currently in red-alert and the squad (or this soldier) hasn't taken an action this turn. (Or have the squad auto-conceal at the start of the players turn if there are no red-alert enemies. The former is better for discoverability, since it puts an icon directly on the abilities UI, the latter is probably less prone to edge-cases/exploits.) This lets players use the combat tools without having to totally abandon stealth. If you can pull off a good ambush, you can kill a pod and then go back into concealment; but between the gunfire/explosions and the corpses the enemies are going to go to yellow alert and get boosted detection and extra reactions, and because the enemies are more spread out you're much more likely to
need to take a shot to clear a path to the objective. Using 'stealth' to clear a mission thus becomes more about setting up surgical strikes when the enemy moves out of position than about staying out of the red tiles until you can evac.
Hopefully this won't step on Conceal's toes too much, since the new reconceal mechanic ideally only works if the entire squad can break contact for a full turn (which should be more difficult with the extra independent groups patroling the map from point one). Soldiers with the perk will still have a significantly easier time going back into stealth. Even if it does, though, I feel that reworking one perk would be an acceptable price to pay as long as the rest works out the way I expect it will.
Point 3 probably will be overpowered in the hands of a shinobi/specialist duo hack squad (hide in a corner, throw flare, reconceal...
), in which case I'd suggest 4) Add a noise rating to throwing the evac flare, and make it disable the default reconceal option for the current turn (or use the auto-conceal at start-of-turn mechanic, which sidesteps the issue). If there are enough (smaller) pods on the map, and the nearby ones go to yellow-alert and come looking when you drop a flare, staying out of line-of-sight through an enemy turn to reconceal should be an interesting challenge rather than a trivial exploit.