The other bloggers involved have argued that removing all outright immunities solves the problem. The design of Dust to Dust is a clear expression of my, and Stands-in-Fire's, position on immunities in games: we're agin' it. At the same time, I can't agree that this is the right tack to take, for a number of reasons. Part of the G+ discussion has been about whether it's reasonable for anything to possess immunity to fire, with some holding that even a fire elemental - that is, again, a creature formed entirely of flame - should be possible to burn, if the fire were hot enough, and others arguing that, if anything, dealing fire damage to a fire elemental ought to cause it to increase in size.
It's interesting to me that one of the commenters and Kainenchen chose the same analogy to argue against immunity: why should fire elementals have fire immunity if a creature made entirely of flesh is not immune to the blunt impact of flesh? I've had a hard time verbalizing why I think this analogy inappropriate, but touching one flame to another - such as holding two lit candles together - damages neither and creates a brighter flame. I think that the vast majority of creatures, and the entirety of spellcasting, should not have access to immunity, but I don't want to entirely close the door to fire immunity as a possible creature trait, for the sake of those poor fire elementals.
I also feel that changing immunities to very high resistance values doesn't address the core problem. Resist Fire 50 might as well be fire immunity, for all that a D&D fire mage can do anything about it. In 3.x, an empowered fireball averages 52.5 damage, and shaving 50 points off of that means that the fire mage can nickel-and-dime the creature to death while just about any other kind of spellcaster operates at full effectiveness. This is why I say that a fire mage doesn't have as much fun as a complete generalist in such fights.
Another proposed solution is a feat chain, magic items, or the like that pierce fire resistance: 5, 10, or more points of it. I'm fine with this, as such, except for the fact that it doesn't help with fire-immune creatures, and the fire mage is paying extensive opportunity cost to be worse off than a generalist by a smaller degree. Also, it's more of a direct attack on a numbers game; the solution I want to see is the fire mage doing something more varied and inventive.
Before I get to my own solutions, I want to be clear - I don't think the mechanic of fire resistance shaving damage off of fire effects directly is a problem. It's simple, it's easy to understand, and it's a pretty reasonable representation of how we imagine something fire-resistant to work; real-world fire retardants can be overcome with more intense heat. Just improving saving throws (so that the target takes half damage more often) is all right, but doesn't do as clear of a job on the simulationist front, since that kind of mechanic more frequently represents avoidance within 3.x D&D. I think that the metagame result of the fire resistance/immunity mechanic - when not paired with lots of other big resistances - is to push players into other solutions. The only problem with pushing players into other solutions is that most games have not included spells for fire mages that do much beyond dealing or resisting fire damage.
My preferred solution, then, is to redefine the fire mage slightly. The fire mage is not someone who projects fire energy to the exclusion of all else; but instead someone who has mastered fire, even when it is not fire that she is projecting. How does she solve the problem of a fire elemental? Perhaps she divides the fire elemental in half, effectively cutting one part of it off from its mystical source of fire. Or she directly attacks the elemental's connection to its home plane. Or she vaporizes the base of a pillar and collapses it onto the fire elemental.
For creatures like salamanders that are strongly associated with fire but not physically formed of fire, the concept of mastering fire still applies: a clever fire mage might well spend a round stealing the salamander's fire and gathering it into her own control, to unleash against the salamander in the following round in an attack made all the more devastating. Sure, that attack might still have to overcome the salamander's fire resistance, but maybe stealing its fire debuffs it in other ways.
In exploring these ideas, it's important to remember to stat monsters with resistance or immunity to fire damage, and not "spells with the [Fire] keyword," since the domain of the Fire keyword to do more than deal fire damage. Feats and magic items designed to boost the fire mage, on the other hand, probably do want to improve all spells with the [Fire] keyword, to encourage the use of fire spells other than damage.
My comments here generalize to other kinds of immunities, but unevenly. If your design credo demands that undead are immune to mind-affecting, then yeah, it's going to be tough for mind mages to do much to them, though at least some players would find mental effects buffing their allies to be sufficient. (I'd love to read blog posts with ideas on how given character themes might address their weaknesses!) I do broadly recommend cutting or rewriting spells that grant almost any kind of immunity - starting with the lowly protection from evil and continuing through mind blank and other high-end spells.
Binary solutions are almost always to be avoided, because it's usually only Sith who deal in absolutes.