That doesn't really answer his questions, since stuff like Code of Princess isn't being published by Nintendo either.
It does strike me as a strange move, kinda. I thought the previous Phoenix Wright games sold decent at least? They've been no huge hits, but I think each sold at least >50k in the US? It surprises me that Capcom does this move without a decently popular game, even though other companies release games that should be selling much less at retail.
I guess they think most of the people who are interested in AA (which is a pretty hardcore bunch), are willing to buy a digital version, so that they aren't losing a lot of sales by not being present at retail while having less of an inventory risk and a higher margin?