Nancy Reagan represented the USA at Prince Andrew's wedding so why not invite Michelle Obama to William's wedding?
I think William and Kate perhaps just wanted to have a different kind of wedding. Yes, first ladies have attended such events in the past, but that doesn't mean they have to be included now.
Besides, the Obamas will be on a state visit to the UK the following month, so they'll be over there for other reasons not too long from now, anyway.