This may not be the answer you're looking for, but...
Last time, we actually ended up registering at both, the reason being that one store would have one item in a particular pattern or style that we preferred, OR one store was slightly cheaper than the other. We didn't double up what we registered for. We registered for the item we preferred at the store that had the cheapest price.
So, for instance, both stores had the bouncy seat we wanted, but BRU was cheaper. So we registered for it there, but not at Target. But the breast pump was slightly cheaper at Target, so we registered for it there, not at BRU.
BRU has a better return policy (or at least used to). Target's return policy was a PITA -- they would only let us return things without a receipt for store credit, if it was an item we'd registered for. Which boggled my mind. If we'd registered for it, why would we need to return it? Anyway, the customer service for returns was better at BRU, but our BRU is a smaller store, so again, it ended up being easier on us (and cheaper for the shower guests) for us to actually register at both places (in addition to online, where we registered at www.nurturedfamily.com
for our CDs).
It's up to you, but there's nothing wrong with registering at both. If you do though, do NOT double up your items at both stores, because then if you get something and have no gift receipt you may be stuck with duplicates, especially if the return policies have gotten stricter in the past few years.