The missile pistol & Commando are the most interesting AT weapons.
And maybe the Epoch too, sometimes, but I couldn't fit that into the title.
Both the Commando and missile pistol exist in a band of damage and AP level that makes fighting heavy enemies more interesting than basically any other normal AT weapon. They have unique thresholds on enemy weakpoints or breakable armor that lets you either get more kills with less ammo or expose an enemy's internal parts for you to shoot at.
The 2-3k damage range on normal AT like the EATs or RR make it so that shooting at a normal enemy is a binary of killing in a single shot or having to waste a second round to confirm a kill. Having AT is important in a normal team, but it sometimes feels like the 'dedicated driver' role of an operation to me. Bringing reliable AT is preferable to the team having an awful time being chased around by five bile titans that take too long to kill, but there's not a lot else to it outside of what exact flavor of instakill you take.
The Commando and the new missile pistol take advantage of breakpoints and random things that basically no regular AT support does intentionally. These two guns are functionally the only two where doing the leg combo on a hulk is a viable thing to do.
Breakable armor in general is a cool way of handling enemy AT and health that barely ever gets used for heavy enemies, and fewer of those enemies make it particularly appealing to kill them that way. Factory striders have AP4 internals despite their armor already tanking AT shots, and Bile Titan armor is just barely tankier than their actual head (while also requiring you to chew through the rest of their main hp). Chargers are practically the only enemy where breaking open the leg armor is more appealing than some other option.
The gulf between AT and below-AP5 weapons could be narrowed with "ablative" enemy armor that can be broken to expose more vulnerable parts. Spore Titans, Warstriders, and even normal bot tanks could have breakable armor that absorbs a singular AT shot without making them absurdly hard to kill with anything else.
I think the missile pistol is a really remarkable secondary weapon, allowing for even more flexible weapon loadouts while not bludgeoning the problem to death like the Ultimatum. You have to put thought into where you shoot the gun, but then you're given a rapid-response AT gun that really like pairing with AP4 (or some AP3) guns. It's not going to solve every problem you have, but it's flexible and strong enough that you don't feel helpless in the way that an AT red stratagem will leave you when on cooldown.
Ultimatum, thermites, and giga-grenades work fine, but are either heavily restrictive in use or otherwise not super interesting outside of clubbing an enemy with 2k explosive damage on their head. The missile pistol is not that much better in terms of raw stats, but it's good enough that I feel like an entire new category of weapon combos has opened up. Especially on AP4 enemies that are otherwise time-consuming to kill without AT.
TLDR; the commando and missile pistol are fun and interesting because they can do fun combos. i wish more enemies had breakable armor to exploit.
also, i don't believe it to be a ""shit gun"". arrowhead couldn't even properly touch the coyote and right now they're more likely to buff the autocannon again or accidentally lobotomize the EMS sentry.