Note: everything is possible with savescumming, these tips are for ironman/bronzeman and just players who don't like to load a lot. Mostly from Commander/Legend difficulty perpective, would work for lower difficulties too.
Patch 1.3 brought upon us a number of changes that made stealth difficult (but not impossible).
- More pods (= more chances to be detected)
- Increased evac delay
- Highly randomized evac position, which can easily be in the opposite corner of the map from the objective
- Drones tend to patrol along map edges, while most other pods hug objective.
- Slightly higher detection ranges & generally nerfed stealth abilities
However, we are up to the challenge!
Generally there are 3 type of stealth approaches:
1) Pure stealth. 1-2 guys, usually specialist and/or shinobi officer. Avoiding combat and detection at all.
2) Distraction. Specialist + Saboteur, which can be a suicide rookie with grenades or a non-suicide Grenadier or Technical (now when you launch a rocket enemies alerted to explosion, not you!) + an optional but highly recommended shinobi officer.
3) Covering fire. It's a new tactic of semi-stealth as now bringing 4 guys instead of 1-2 barely affects infiltration time. Basically you have your specialist to hack door/chest, an officer to command him and 2 other guys to cover his retreat (you want guys with area control, like grenadiers with smoke/flashbangs, gunner ideally with iron curtain, technicals etc). Generally you set up your squad so you can ambush a pod (that guards the objective) and at the same turn hack the objective and start a retreat toward evac. Resist urge to actually fight enemies, just control them and run outta there. The best thing, you can actually plan for variant 1 or 2, your other two guys are insurance in case something goes wrong. Only works with fixed evac though.
Jailbreak
Pure stealth: not viable anymore in 99% of cases. Evac is usually far away across the map, enemy pods like to patrol jail cell area.
Distraction: 20% chance of success, high chance of catastrophic failure (wipe). Only works if evac is nearby. Jailers pod seems to be hard to pull out from the building with distractions (mayhaps walls block sounds???) Not recommended.
Cover fire: did not try actually, but might work. Again Evac should be nearby for this.
Verdict: forget stealth, go loud with 4-5 soldiers, safer that way. RNFs start ticking at the turn 1 now, so no real reason to even stealth towards objective. Just engage enemies at 1st or 2nd turn and push towards cells.
Free transported prisoner
Very similar to what we had in 1.2 actually. Pure stealth possible, but very risky. Distractions work fine though, but you have to get lucky with enemy positions. Bring smoke!!! Cover fire best way to go, as pod patrolling around the van is easily ambushed. Frost grenade (from Alien Hunters DLC) works wonders here. Remeber standing near the closed door in the back of the van with your VIP counts as peeking around the cover! Better open the door with your concealed shinobi first.
Extract
Unlike 1.2, now we have RNFs waiting for you right from the start, dropping around turn 6-8. And yes, they WILL drop on the head of your revealed VIP. On top of that civilians now can not be commanded or OscarMiked. So single shinobi officer tactic works no longer (unless you get real lucky). Distraction could work, but you need a technical or grenadier who rolled phantom in AWC, or send in multiple shinobies with grenades. I would ony recommend this for really important missions though, like a liberation chain. Combat is better option here 99% of the time.
Hack chest/laptop in train or facility
These are actually almost unchanged from 1.2. The only real difference - increased evac delay. But there are few tactics to combat this:
1) Standard pure stealth (solo specialist or specialist + shinobi, ideally officer)
Approach objective along the map edge. Find a spot where you can hack objective remotely (Gotcha again ruleZZZZ!!!) AND where you are not in the line of view of any enemy AND where you can blue move (or yellow move if you have an officer with you) in a line-blocking high cover (building, van, fence). You need to start your turn with your specialist in the spot and there should be no enemies in his line of sight. This may take a few turns waiting for an opportunity and a bit of luck. But remeber you have 8 turns, of which you only need 3 to get to the spot usually (plus officer intervention). So in about 75% cases it can be done, almost safely, especially after you get the feel how enemy patrols generally move (comes with game experience). After retreat - you must not activate any pods! - throw evac and hunker for 6-7 turns it takes to arrive. Remember, after you hack the objective nearby pods (if not all) are alerted of the spot where you hacked from and rush there to investigate, so your hiding spot must be out of sight vs. possible directions enemies might come from. Usually it is something along the map edge. And if the opportunity to hack will not manifest until timer runs out you can just safely retreat in the opposite corner of the map and extract. I recommend this tactic if you don't have time or manpower to infiltrate 5-6 people for combat.
2) Quasi-Suicide specialist tactic. I never tried this one, but got the idea from xwynns' video. Apparently you need a specialist with PCS "Life support" which gives +3 turns to bleedout time, and a shinobi (shadowstep ability required, officer not necessary). Position your soldiers nearby objective. Run specialist towards a spot where he can hack remotely (ignore enemy presence and cover). Throw evac under your feet and hack the objective. Sit there to be killed. When you have just one turn left bleeding evac should arrive (so it only works if evac is 6 turns or lower). Move in with your shinobi (most enemies would be on overwatch, hence shadowstep requirement), pick up your buddy and evac. Mission accomplished! And your specialist is out of action for a month, but who cares! If evac delay is more than 6 turns you will probably have to sacrifice a specialist. When he dies Data will (probably) drop as an item that you will (probably) be able to pick up and evacuate. So if you have a really important mission (blocking nasty event for example) and too little time left you may try this underinfiltrated, as this tactics may work even with swarming enemy presence.
Destroy Relay
Two snipers and a shinobi scout can still do that without activating pods (unless Relay is wierdly positioned where you can not get a line of sight on it from across the map, in that case just abort the mission). Just be sure to have smoke grenades on your snipers and their rifles equipped with best available silencers (to not attract pods walking around).
Capture/Kill VIP (vehicle)
Capture is much more difficult now as shinobis can not reduce VIP visibility to zero (need confirmation on this one). If you want to capture, go in loud or cover fire/distraction (did not try those myself yet).
Good old sniper kill still works. Be aware though that all enemies will rush toward your sniper after the VIP is dead (even if you did not activate any pods!), so commanding him after shot to retreat towards evac might be a good idea.
Capture/Kill VIP (building)
Did not encounter this in 1.3 yet. Should probably expect pods bodyguarding VIP.
Smash&Grab
Do not even try
)