I can't tell you how many times I've been fingerprinted. Most recently it was for my CHL, but most of the time my prints were taken for security clearances. The idea is certainly NOT to verify that you are who you say you are, but rather to see if someone with your prints was involved in "bad" things. As pointed out above, fingerprints are forensic evidence.
As for iris scanning not standing up well enough, so as to give anyone leverage to say "you need a chip because iris scanning can be fooled," before it's used formally and extensively, that sort of issue has to be laid to rest. Irises are at least as unique as fingerprints, but there is to date no formalized and universally recognized method of collecting iris scans and comparing them-everything today is proprietary. Before accepting iris scanning as valid ID, the technology would have to be 100% accepted as completely foolproof, at least as valid as fingerprints. That won't happen for a while, and when (not if) it does, the issue of microchips will NOT be a factor.
Side note: what about when you're 85 and have Alzheimers? Chips to help identify people with Alzheimers are in use right now and are actually saving lives. Not all of these technologies are the stuff of "black" agencies you know.