Children's ministry programs are one of the great church innovations of the twentieth century. Sunday School classes have existed for far longer, but the complete children's church experience -- removing children from adult worship entirely and placing them in a worship environment designed specifically for them -- is quite a recent phenomenon.
Even more recently, perhaps in the last three to five years, the pushback against children's church has emerged. The first kids who were raised in those programs have now become adults, and the studies about those adults are in -- with mixed reviews. The majority of the research I've seen suggests children's church programs may actually hurt more than they help. Children can feel isolated from the rest of the church, fail to fully integrate into adult worship with its different songs and rituals, and ultimately leave the church entirely since it's not like what they loved growing up. Some reports say programs which mirror adult worship but keep the vocabulary on the kids' level do much better. Still others (a definite minority) list no negatives for these programs whatsoever.
It's become a divisive issue, honestly. For our part, RSCC has begun a sort of compromise position: our kids stay in adult worship for everything but the sermon, then go to children's church for a lesson prepared just for them. Our monthly Family Sunday allows them to stay in "Big Church" all day.
Regardless of your approach, take care of your children. Teach them about Jesus. Train them to worship as adults. And in all things, lead them to the cross.