My theory is that they ship the number of copies based on the number they want to ship and the number retailers order and the number of copies that is shipped is somewhere between the amount the publsiher wants to ship and the number of copies the retailer ordered.

It's what retailers order, but publishers usually push retailers into ordering more.

It's tough to send out copies of new ips or just unpopular ones.

it's completely up to retailers how many they want to order, the retailers are the ones taking the risk on buying the game. If they have to sell them at a discount they could lose money, if they don't get enough they lose potential profits.

Because the series in Japan is wayyyyyyyyyyyyyyyyyyyyyyy ahead than what the time frame in the game is.

Im sure naruto will hit 40-45,000 first week, not too bad lets face it, considering they only shipped about 50,000

shipments has nothing to do with company expectations, only retailer expectations.

if publishers had their way they would ship millions for every game

Not true.  Many games aren't even expected to sell 100K lifetime let alone 1 million copies.

But that wouldn't be the publisher's problem, it would be the retailers...  That is assuming the publishers don't sell on consignment, which I doubt few do...

Is there any info about Disgaea 3 best of ... edition ? Or we don't get any sales info for those normally in first day sales ?