Obviously this is the first DOA for a Nintendo platform. We wanted to commemorate this occasion with something so we decided to feature a stage crossover with Other M. The footage we released for this was a bit confusing because it didn’t allow us to show our true intentions behind having this stage in there. One thing about Samus as a playable character — for DOAD our aim was to have a compilation of DOA characters so we purposely left out any new or guest characters in the game. Samus is a lone bounty hunter and protector of the galaxy so we thought it would be better to let her focus on her job rather than kicking everyone’s butt in DOAD.
That's what the devs said, at least according to an interview on IGN. Basically, they thought it wouldn't make sense, and that there should be no guest characters.