Thunder Thunderbolts. Their large size makes them perfect for deploying mine fields. Or other submunitions for that matter.
DPCIM Thunderbolts? You're giving up the concentrated damage, but in return you get to pound everything inside a target hex with cluster bombs.
Streak Thunderbolts. To avoid out of control spiraling tonnage costs, Streak Thunderbolt missiles reduce some explosive payload in favor of additional guidance control equipment. They're large size and already considerable payload allows this.
Armored/Armor Piercing Thunderbolts. Mounts extra armor on the missile that reduces effective range and the number of missiles you get per ton, but all but guarantees the missile to be immune to AMS while also allowing a better chance of penetrating intact armor.
Nuclear Thunderbolts. Just because. :D
I'd argue that since Streak guidance doesn't affect warhead size on a SRM, then it won't affect the warhead size on a Thunderbolt.
But I'll add Swarm to the list above. Essentially, you roll to-hit against the target. If you miss, you roll to-hits against closer targets until you get to the limit of Swarm radius. Essentially the same rules as current Swarm, just without rolling on the Cluster table.
As for Thunderbolt vs artillery comparison, Thunderbolt missiles do less damage, have shorter range, and mass more than an Arrow IV missile. The Thunderbolt-20 masses the same as IS Arrow IV launcher, but is 1/3 the size, so the launcher making up the difference (somehow) isn't possible. Thunderbolt-15 is 1 ton lighter than the Clan Arrow IV, but only 1/4 the size.
Personally, I'd be happier with Thunderbolts getting more damage per ton of ammo than LRM (180 pts/ton?), due to larger missiles being more efficient than smaller (only one guidance system needed, surface area determines drag vs volume determining fuel supply/warhead strength).
Of course, AMS would still shoot them down. Perhaps a jammer pack could be developed for Thunderbolt, so AMS requires additional shots due to shooting at decoys, or is less likely to shoot the missile down?