The shotgun should take the top spot as it's able to punch directly through shields and one-shot every NPC. The spread can be managed with the hipfire accuracy and scope mods which both act like chokes, giving it the same effective range as the executioner but double the power.
I agree with the rest of your post though, and would add that while different resistances works on spaceships with multiple hardpoints that can be used simultaneously, on foot it just feels ridiculous before you even get to the balancing issues... You're telling me that in the grim darkness of the far future nobody thought to do a Ripley and duct tape a kinetic to an energy weapon? Everyone's really going to keep hot swapping like space jugglers? It's clearly and greatly inconvenient (edit: also from a gameplay challenge perspective it's not difficult or interesting enough to warrant it, just makes everything feel stilted.)
Lots of FPS games do well with fast weapon switching, like DOOM with its vast arsenal, but there you switch for fun and efficiency in a cartoonish setting, and will use one gun per kill, not because you're forced by a boring rock paper scissors system that requires 2 guns per 1 enemy in a pseudo-realistic space setting.
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