Immunity to Normal Weapons still suffers from AP though. You mention Ares Alphas, with APDS that's 11P/-6 and thus it will always pierce the Immunity. So let's assume they hit with 1 net hit, that's 12P/-6 vs 8 Body, 16-6 = 10 Immunity, 5 hits on the Armor spell. So 8+10+5 soak, and 10/2 = 5 autohits. At 1 net hit it's ~1/3 chance to actually do damage, with 2 damage done average on a hit. It's a dogfight at that point. A Magical Indirect Combat Spell would solely face 8 Body and 5 Armor from the spell, and he only has that 5 Armor against any non-Physical attacks.
If he doesn't have Armor, hitting will be far more difficult due to the -2 sustaining penalty not applying. A damaging hit will be more likely then, but only if they still manage to hit and then they likely would have done more damage (due to an extra net hit) in the first place. I'd use the Armor spell, it makes sense from the doc's perspective. And 3 net hits instead of 1 already is 2/3 chance to hit instead.
As for destroying the Shipment with a single spell, first of that's a bit of a silly move for the doctor since he cannot easily recover from Drain, while the crates may very well be resistant enough to not lose everything inside on the first attack. And he also should focus on his enemies. As for Toxic Wave, it just fits more with the environment y'know?
If you think the players lack the kind of tricks needed to hit him, consider making him show up completely alone. But please stick to the designer intent that he has Immunity, because as you say otherwise it's far too easy. It's the climactical boss fight, and you can always make John wake up and join the fight if that doesn't work.
The problem is that while one Street Samurai can do minimal damage through the Immunity (one uses APDS, the other uses Explosive ammo), the rest of the party has a tougher time in the fight. The second Street Samurai's explosive ammo will bounce against the Immunity (12P, -3 AP). The Face/Decker only has a light pistol, which means the only thing he can contribute is grabbing some of the serum and running. The Mage will be taking -4 on his spells, which means he has 8 dice for casting (Spellcasting 6, Magic 6, -4 penalty), and not the greatest selection of spells versus the Doc (he normally uses Control Thoughts or Ball Lightning). The Gunslinger Adept's main weapon is a light pistol, though fortunately she just picked up the Cavalier Arms Crocket EBR in Ashes and loaded it with EX - Explosive (14P, -4 AP) - which does enough damage to not bounce. However, she's taking a -3 die penalty (she has Improved Agility 3 that she'll probably turn off) and no full-auto to help hit. John, by the way, is useless against the Master Shedim if Immunity is in play - the machine pistol will bounce, as will his unarmed attacks.
My concern is that I don't want the fight to be fun only for a few characters...and I want to be consistent. If the Master Shedim has Immunity, so will the normal Shedim, which
completely changes the first fight. I'm perfectly willing to bring in normal Shedim for the final fight if balance is an issue, but I'm on the side of the fence that feels the 5E Shedim don't have Immunity based on my reading of the rules. Plus, this shouldn't be TOO long of a fight...even with worrying about Drain, the Doc's AoE spells can quickly turn this into a TPK. On average, the Doc will get 5 hits versus drain, and can spend Edge to reroll failures. The first spell he throws will probably be a Force 8 Ball Lightning. By all rights, he should spend Edge on both the spell and the Drain resistance test, but I'll only have him do so on the latter.
Now, if I remove the Immunity, it makes far too much sense for the Doctor to have previously bought some Armor Clothing (or has stolen some from a victim). I could go so far as to give him a Lined Coat without unbalancing things - it's less than 1000 nuyen, and it gives him a good soak
Shipment - With a Force 8 AoE spell, it's quite likely the Doc can hit the shipment AND at least some of the PCs. Or, if he wants the shipment destroyed and is worried about Drain, he can cast it at a lower Force twice...which should still do enough damage to destroy a bunch of glass vials in boxes.
Toxic Wave versus Ball Lightning - Toxic Wave is overused in Missions...it seems like every spellcaster has it. I wanted something different, and the Initiative penalty effectively gives the Doc more chances to act.