Enhanced Edition is so enhanced, the poor bot teammates Barachiel (Heavy Weapons) and Nahum (Apothecary) can't handle it! I play special missions a lot and it's really frustrating to see them constantly dying.
First, they can't be upgraded. In the campaign, you could unlock 20 percent more armor for them and 70 percent resistance to killing blows via the command skill tree, which made them very durable even on No Mercy difficulty. You can't do that in special missions. You also can't give them any of the awesome new perks and gear upgrades that come with Enhanced Edition. This means they are very squishy and there's nothing you can do about it.
Second, they can't deal with the new Bioblast-strains. These screaming purple acid suicide bombers do huge damage in a large radius and must be shot down before they reach you. However, the bots don't prioritize shooting the Bioblast-strains and end up taking a lot of damage from them. A player can improve their armor with 20 percent bonus armor and 50 percent acid resistance to mitigate the threat somewhat; the bots cannot.
Third, they can't deal with the large numbers of Stalker-strains that spawn in Enhanced Edition. These stealth hunters will leap out and strike for huge damage. I have learned to be wary when the minimap gets jammed and will either look out for the shimmering outline of an oncoming Stalker-strain or will recon by fire, spraying the area with shots to force the enemy to reveal itself. The bots have never been smart enough to do this. Even if they are facing the right way and there are no other enemies around they will just stand there and get stabbed in the face, often killing them instantly. Even with constant tactical management, it's hard for me to keep the bots alive if they can't even see enemies that can instantly kill them.
Fourth, the bot AI is very basic. They simply attack. Melee bots don't hold position (even when displaying a solid shield symbol, indicating a "stand ground" command), chasing after enemies forever and leaving their team exposed. Ranged bots constantly fall out of formation, lagging behind to shoot enemies or pushing forward to engage and getting in the way. When I'm backpedaling to avoid a Stalker-strain's leap attack, Nahum will rush forward to shoot, take a scythe to the face for 90 percent of his health, and end up blocking my line of fire so I can't save him. Barachiel in particular has great difficulty in using his assault or plasma cannon because of wind-up time (even though the plasma cannon doesn't actually have any wind-up time, he takes forever to start shooting with it).
The combination of squishy bots and very basic AI means that special missions can become very frustrating affairs, even on normal difficulty. The bots are completely unable to survive unless I play one very specific load out: giving Nahum and Barachiel thunder hammers and storm shields (or lightning claws). Nahum can't heal if you do this, and Barachiel won't have a gun either, so I need to play Apothecary to heal and to shoot hybrid and turrets. That means skipping out on 90 percent of the content just to have teammates that don't die constantly.
If it's not possible to make the bots smarter, please consider making the bots tougher. At the very least, let them be as tough as we can make our own characters: 20 percent bonus armor, 50 percent acid damage resistance to help with Bioblast-strains, and 30 percent more health per body part. Resistance to Stalker-strain leap attacks would also go a long way towards increasing their longevity and thus effectiveness.