Actually, I think there are a few things that should be pointed out WRT the single target nature of the spell:
First, it is not true that only single targets have spell resistance. The 8th level cleric spell, Unholy Aura (and all of the other alignment auras) affect multiple targets, grant SR 25 (not negligible until the highest levels), and are at will abilities for a lot of the higher powered fiends. So, a single balor with an escort of Vrocks will not be the only foe with noticable SR. All of his attendent Vrocks (and Babau, etc) will generally have Unholy Aura SR.
Even without adding spells/abilities like Unholy Aura into the mix, groups of extra-planar foes will generally all have spell resistance--and if they are tough enough to be noticable threats, they will generally have SR that works 20-30% of the time. For instance, an evil 10th level wizard facing a group of hound archons (and it takes 8 hound archons to be EL 10, so something along the lines of an Astral Deva and 8 hound archons would, in theory, be a moderately challenging encounter for that 10th level wizard's evil party) will have a 75% chance of getting through their SR without feats. While that's not bad odds, it's definitely a noticable advantage for the celestials--and a noticable advantage that Assay Resistance won't help to counter but Spell Penetration will (and in spades!).
So, as a single target spell, it is useful and powerful against single-opponents, but Spell Penetration still has good yield against groups of foes--and foes like the hound archons without the Deva who, individually have annoying spell resistance but don't have enough to justify using Assay Resistance on.
There is also another disadvantage that has not been mentioned here:
Assay Resistance costs a swift action and characters only get one swift action per round. My high level fighter/wizard will cast a quickened spell nearly every round of a serious combat. My mid-level cleric will often cast a quickened spell and will do so with increasing frequency as he gets more high level spell slots. This factor comes into prominence as the cost spell slot cost that Auraseer analyzed fades in significance. For a 14th level wizard, a 4th level spell slot may not be a big deal. However, by the same token, he may well have quite a few quickened spells prepared. Casting Assay Resistance means forgoing the quickened scorching ray, quickened ray of enfeeblement, quickened haste, etc.
All told, I think Assay Resistance is still a very strong spell. But it pays not to overestimate its strengths or underestimate its weaknesses. Any character specializing in area effects, will find the single target aspect a large disadvantage since it renders it useless for his specialty (cleaning up the yard trash). A character who forgoes spell penetration will regret in every time he loses a spell to SR against a creature that isn't enough of a threat to merit one of his Assay Resistances but is big enough to use second or third tier spells on. And a character who uses quicken spell extensively will find the opportunity cost of Assay Resistance a bit rough (especially since the fights where it's worth using it will generally be the kind of "pull out all the stops" fights where he'd ordinarily be casting two spells/round).