The Metal Gear Solid HD Collection on the Vita outsold MGS3D on the 3DS by a massive margin and cost quite a bit less to produce since the system's more powerful and has better devtools. Third-party game sales on the 3DS are abysmal, and third-party game sales on the Vita are great considering the small install base. Pretty much anything that isn't Mario or Pokemon isn't going to be purchased by the average 3DS gamer, the numbers prove it. It's not as simple as "there are more customers on the 3DS!"
Update: geez, four posts in a row. I wish I could somehow respond to four comments without bumping this thread four times, that's not cool.