If you want to do Peds ER, why would go through a combined program? Do Peds, and go on to Peds ER fellowship, or do ER, and go on to a Peds ER fellowship.
Honestly, I don't get these combined programs. Hard to believe the fad will last long.
There are a few reasons why you might want to do a combined program instead of a fellowship. Let's say you're a peds resident interested in emergency medicine. Do you do a fellowship or a second residency? They both take three years. One isn't necessarily better than the other - they are completely different training. True, you may be able to get a job in a peds ER with either set of certifications, but there's no guarantee how long it might be before children's hospitals want only fellowship-trained doctors.
But what if you aren't interested in living in a large city with a children's hospital? It's pretty tough for a pediatrician to take a sub-board certification into a community hospital, simply because most don't have the volume of pediatric visits to support a peds EM doc who cannot see adults. But a physician with dual-board certification is highly desirable to those same groups - they often need another general EM doc who has peds experience. True, you could do an EM residency and then a peds fellowship and still fill this position, but what happens if you burn out down the road (as many EM physicians do)? If you had done both residencies, you would have a full certification in peds to fall back on.
Also, many dual-board certified attendings keep appointments in both departments, or work primarily in an ED but also do some work in pediatric clinics, so it's not entirely true that one certification goes to waste. (See "A survey on the graduates from the combined emergency medicine/pediatric residency programs."
Journal of Emergency Medicine. 2007 Feb. 32(2):137-140.)
So if there is some value in having certifications in both EM and Peds, which I think there is, then a combined residency is a good choice - it saves a year, it offers a stable five years instead of having to match all over again halfway through, and it allows you to learn both fields simultaneously, instead of concentrating on one field and then forgetting it as you throw yourself entirely into another one.