There are quite a lot of things that players are immune to, and some that monsters are immune to, although the latter has been reduced considerably; however, lifting immunities on monsters has created something of an imbalance in some parts of the game due to some abilities being overly dominating. Ultimately, this all comes down to immunities restricting options and narrowing gameplay when used too much, and to not having a good middle ground in place between being immune and not being immune.
For instance, Freedom of Movement becomes a fairly common buff by around level 15 or so, when divine casters have enough spell slots to keep it loaded and enough mana to keep it up on everyone throughout a quest. Having FoM on means that enemies and traps that would hamper or prevent movement have no effect, and are rendered rather pointless.
The response the devs seem to have taken to counter this sort of problem is to have more monsters using Dispel Magic and by including Disjunction traps. That works in some places, but it gets rather annoying. Another solution the devs have initiated has been to remove an effect (earthgrab) from the list of things prevented by FoM.
In the case of Fortification, enemy striker types (rogues mostly) have had their sneak attack replaced, or augmented, by simply scaling up the damage these creatures deal to compensate for the fact that they cannot sneak attack most players. We've seen some Fort reducing effects added to enemies' repertoires, but those are fairly minor and uncommon. We have more ways to debuff our own Fortification in order to gain some buff or another than enemies do.
What we've ended up with are situations in which players are free from most forms of non-damaging harm (FoM, Greater Heroism, Neutralize Poison, Disease Immunity, Resist Energy, Heavy Fortification, Death Ward, Deathblock, Blindness Immunity...the list is pretty long). Sometimes these get stripped by a Dispel, or death, but much of the time, players are running around immune to most weapons you can bring to bear on us that don't deal straight, consistent damage. That takes a lot of variety out of the game.
There has to be a middle ground between our being immune to something for 20-40 minutes for 50 SP or less, and not having a resistance against it at all besides our saves. I'd be interested in seeing ablative immunities, or effects that instead of granting immunity instead allow rerolled failed saves or no failure on rolled '1's, or shorter duration buffs, of ways for enemies to suppress our buffs, rather than getting rid of them entirely, or...something.
On the monster front, I'd prefer to see better encounter design, where more groups of enemies come with a buffer that tosses out things like Mass Death Ward, or sings the Greater Heroism Warchant song as their opening moves. Give us the ability to stop enemy casters from buffing their allies, and of sometimes being able to debuff enemies that have immunities, while ensuring that we cannot simply Wail of the Banshee, Circle of Death, Finger of Death, rinse and repeat, because some enemies will have immunity...from a spell or potion.
I much prefer the few encounters we have that push us to try and stop the enemy casters from getting their spells off, or approach the encounter in a different fashion. The first fight in Chronoscope is like this--when I'm soloing for scrolls on my Pale Master, my first priority is to kill the teifling cleric before it can cast Mass Death Ward. If I succeed, I spend about 1/3 to 1/2 of my SP clearing everything in that first fight, and finish in 2-5 minutes. If I fail at that, I spend 1/2 to all of my SP and finish the fight in 5-10 minutes. If I were to carry Greater Dispel Magic, I could mitigate that problem, perhaps, but the dispel check is rather high, I believe (can it be made? I always forget to prepare it).
The problem with the Chrono fight, though, is that we both know about it and are given time to set up for it. If we had some more randomization in what we fight, some of the power of metagaming would be offset. If we didn't know which of the figures sitting around that circle would become the cleric, we'd have a harder time in there. If we didn't know whether, when getting to the locked door in Epic Tharaask Arena whether we'd be fighting 3 ogres and 4 trolls, or 2 ogres, 3 trolls and 2 ogre mages, we would be caught by surprise more often, and would be more significantly challenged, and in a non-cheesy way.
Ultimately, something has to be done about immunities, on both sides of the DM screen, in order to improve the health of the game and make it more interesting.