In rough order of importance:
1. Spells that fix problems you have are almost universally subject to SR, which means that Lycanthromancer's example above is a thing that happens.
2. Instantaneous Conjurations ignore SR. This was a fluff decision that makes a large number of spells that were already good even better. A side effect is that magic immunity and the like is not the kind of defense it should have been, making a lot of monsters that have it over-CR'd.
3. Likewise, spells that affect your surroundings can still fuck you up; no matter how high your SR is, grease can still mess up your day.
4. The numbers are really hard to manage because of CL boosters and short-term duration effects that give ludicrous bonuses to SR checks. It's difficult to come up with a number that won't be impossible for a Wizard who isn't trying, but still allow a Wizard who is trying to have a chance to fail.
5. A personal problem on my part is that it's completely binary, and because of the above problem, that leads to problems. It's really difficult to have an SR value that matters; your options are either it is ignored (it's easily overcome or the player bypasses it with SR: No) or it shuts down an entire archetype (which isn't fun, especially given that it becomes more or less ubiquitous past level 15 or so, at the latest). This is a problem that can be dealt with by resolving the others, however; the impact is minimal if, over the course of a battle, the caster is likely to get at least a few spells off.