During the development of 4e, I argued against including resistances against energy types. My argument was pretty simple:
Resistances create a disparity in value between energy types, but only if the DM uses a particular mix of monsters. Fire attacks blow in the campaign that has lots of red dragon and azers, while cold attacks such in an arctic campaign.
Story-wise, resistances mess up intuitive themes. Take my second example from above. If you were playing in an Arctic themed campaign, you might think it's a cool idea to play an ice wizard. Well, if you're fighting lots of ice creatures, that's actually a terrible choice. The folk of the frozen north should study and use fire magic. The desert nomads use ice magic. Sure, you can explain around that, but it's a jarring inconsistency. I'd rather have the flexibility to do it how I want.
Now, there are some story reasons for resistances. The fire elemental can walk through magma without harm, but you can easily get around that by placing all the mechanics in the right place. For instance, the elemental might have the "magma born" ability, which lets it ignore fire damage from terrain.
In place of resistances, I prefer two mechanics.
First, I think it's OK if a monster has limited access to damage denial. Maybe once or twice a combat it can reduce the damage from an appropriately themed attack.
What I'd prefer, though, are special abilities and bonuses that trigger when you use the "wrong" energy type. Blasting the red dragon with fire hurts it, but it also lets the dragon use its breath weapon again. Using a cold attack on the frost knight gives him +5 AC for a round. Blasting a ghoul with necrotic energy gives it an action point.
I like those sort of drawbacks because they make battles more interesting. You can try to finish the dragon off with your fire attack, but you risk giving it a powerful counter-attack. You can more easily dial the power of such abilities up or down, whereas resistance in even its weakest form (resist 5) is powerful at low levels and still quite useful at epic.
So, that's my stance on resistance.
Things that are lost
2 hours ago