The CR/EL system works, though how well varies from group to group and situation to situation. There are some core issues that need to be recognized, though.
1) As mentioned, the 'core-four' are assumed present, and CRs were computed assuming that certain capacities would be within the PC's grasp. I've long believed that many undead would be CR+1 if a cleric isn't with the party. Ghouls/Ghasts, Bodaks, Devourers and others, for example, feature powers that are potentially TPK without a cleric's protections.
2) When most people review the system, they're really talking about CR and ignoring EL. This is like talking about a car's performance, but without discussing the surface it drives upon. Determining the EL is, regretably, like voodoo sometimes. However, it's necessary. Someone mentioned a wizard with summoning spells above: implicit, I think, in his example was that the wizard HAD ALREADY SUMMONED some monsters as part of an encounter. CR is the same as if you surprised him, perhaps, but the EL is radically different.
3) The CR system depends, implicitly, in the veracity of the numbers assigned to the monsters. And these numbers weren't always correct. The Ogre as a CR2 creature, for example, was off. Further, since 3e wasn't tested nearly as extensively at high-levels as it was for lower ones, CR is less dependable at higher levels. And since monster creation under 3e is primarily a matter of 'compare it with existing monster X...does it seem about as powerful?', there's going to be errors or misjudgements.
4) The CR/EL system is a guideline, not a guarantee....and in a game that uses a pseudo-random number generation technique like dice-rolling, odd things will happen. We call this the 'Everybody Rolls a '1' Eventually' rule. I had an 18th level party destroy a CR23 Winter Wight...because he was arrogant and after literally 20 spells were thrown at him, he rolled a '1' and was destroyed.
5) The ER/CL system under 3e doesn't handle mixed groups or large groups well, for calculation purposes. Computing the EL of an encounter with a mixture of four different CR levels with some having multiple creatures can be difficult to accurately gauge their threat level.
All of which is to say that the CR/EL system under 3e is a pretty darned good tool, when used with the proper mindset. Some folks have worked on improving it for years, now. WotC attempting to supplement it is a laudable goal, and I certainly believe there are lessons to be learned from past work and improved upon.