Anybody else feel bad for Stardock trying to reconcile stuff like this?
Not really. 
Looking at some of the other threads, I've noticed Frogboy can say something like 'Soverign Death is Non Negotiable' and then... the thread will be filled with people trying to negotiate ways to get around it. There's people with conflicting opinions on every topic.
Ultimately, the developers have to make a choice based on what they think makes a better game. And that's what they get paid for, so I'm sure they're most qualified to actually make the decision. I can just say what I think, and there's enough different opinions being thrown around that I don't feel the need to argue too strenuously. But even so...
So the enemy troops are wearing pansy little amulets that protect them from 6% of your fire damage... It's not like your volcano, or even your fireball, all of a sudden isn't gonna work.
But that's just it... there's two sides to this whole thing and *both* are getting trumpeted as reasons why this sort of system (the rock-paper-scissors relation between elements, not simply having damage types. I admit I'm off on a tangent from the conversation here) works.
One person's saying 'I can make Amulets of Fire Resistance, and protect my troops from fire magic!' And you heard my response to that - if it's so easy to make something that protects from one element, then you're better off dabbling in all five. It is always the case in these rock-paper-scissors arrangements that specializing puts you at a disadvantage because your opponent can always counter with whatever option beats you.
But on the other hand, you're absolutely right. It can easily be that 'fire resistance' is a rare and difficult thing to get, and you can't produce amulets of sufficient power or sufficient quality to protect your troops. But in that case the amulets themselves are worthless, because you spent extra turns and extra resources building a unit that still got destroyed by a volcano. May as well not have had the fire resistance at all.
Neither of these are particularly interesting scenarious, are they? I certainly lean towards the latter, because I'd rather have a choice of which element I'm going to utterly dominate my opponents with than be stuck trying to figure out which element their current batch of troops is weak against. Because these simplistic models always, always result in one optimal strategem, which is 'use whatever element beats the element your opponent is using'. In the long term, I can't see how a strategy of 'keep using Fire magic, because I like Fire Magic, and I don't want to split my research' can be successful when the other guy can switch to another type of magic that beats it.
I think the logic of having elemental damage types is actually quite transparent. It's, hey, this old game that I liked used a system like that, so it must be a good idea, we should do it. The idea makes a degree of sense, it's got traction in plenty of other games, and it's an easy thing to do, so why not, right?
But I do sort of think the arguments that are being put forth for how important it is are... well, based on some pretty tenuous assumptions.
Just to restate examples others have already given, and to give a few of my own: without magical types and resistances, how do you make it so that fireballs don't affect fire elementals? That dragons take minimal damage from fire? That Ents are particularly vulnerable to fire? That a desert-dwelling human faction has some minor natural resilience to fire due to their acclimation to the desert climate? That troops wearing hot, heavy armor won't be as bothered by a chill wind as the guy in light leather armor next to him? Resistances are not necessarily something that will only affect a rare creature here and there. It is possible to make them that way, and i that were the case I'd say it's still worthwhile - just have resistances not show up unless they're nonzero!
Okay. So.
Fireball, fire elemental. Reasonable enough. Assuming any Fire Elementals that are in the game are probably summoned by Channelers with Fire Magic in the first place.
If Dragons are supposed to be powerful they should be resistant to more than just fire, shouldn't they? Give them 'magic resistance' and that will do the job, won't it?
Now Ents. Don't get me wrong, I love Treemen, but Ents. In a blasted post-apocalyptic world mostly drained of magic? Where are they supposed to be hiding? Where do we get the idea that they're a part of the world that the game should be designed around them?
Desert-Dwelling Humans with Fire Resistance? I think it's a silly fantasy trope. Starving children in africa are not mysteriously imbued with inflammability because they happened to be born in a hotter climate. But that aside, I've seen the list of civilizations for Elemental, and none of them look like they're candidates for this sort of super-specific bonus.
Armor that has an effect on whether or not the character feels a chill wind. Is it really feasible or desireable to have the game model weather conditions to the degree of having characters experience personal discomfort? Unless we're talking about a sorcerous chill wind, in which I question whether or not air magic is necessarily going to care what you're wearing.
Now, of course the reasonable answer to all of the above is 'Well, obviously somebody is going to want that. Let them mod it in and put elemental damage types in the base game to make it easier.' I'm fine with that. But the sort of game these examples hint at is really fitting with the image I've got of the setting. -
I think I explained why I don't like Rock-Paper-Scissors. But just to go into more detail with the magic...
Obviously the idea here is 'well, water beats fire because fire is extinguished by water'. But you can also put out a fire by covering it with dry sand, and I'm sure you've blown out candles before. Why don't Earth and Air get bonus damage against Fire? The only element that doesn't defeat Fire is Fire, except, wait... you can start a back-fire which steals oxygen from a fire and makes it burn out more quickly.
And on the reverse, Fire can boil away water into steam, so fire should just as logically get bonus damage against Water. Fire absorbs oxygen and creates smoke, so maybe it should get a bonus against air? And stone will burn just like anything else if you get it hot enough, so... you get the point.
If Water beats Fire, what does Fire beat? Ice? That's not one of the 6 elements, and besides, it's just silly. Ice melts and becomes... water. Which beats Fire. Wood? Also not an element, unless maybe you shoehorn it into... Life, or Earth. And then what beats Water? Air? Earth? And which of those beats the other? The thing is, there's not some clear-cut elemental cycle that fits in with your ice-creatures and your wood-creatures and the rest.
So really... I'm totally willing to go along with, yeah, this creature or that creature can have a particular elemental weaknesses. But those would probably be rare, and in any case they're specific to that creature, rather than part of some generalized rock-paper-scissors scheme where you give a damage bonus to element X when attacking element Y.