The following answers come from Super Mario 3D Land Director Koichi Hayashida...
Why Bowser and Boom Boom were included...
"The fundamental question that we start with is "what type of gameplay do we want to create?. We created a test in which Bowser blows flames from in front of the character in 3D space, and we liked it, so we decided that we wanted to have Bowser appear multiple times. ...when Tanooki Mario appeared, some members of the team wanted to include Boom Boom and the Koopalings. Then we created a type of gameplay where the enemy follows as you run around the room, and we thought this would be interesting, so we used Boom Boom to put it into the game."
How the Zelda level came to be...
"The Zelda tribute level was born from tests we did to determine what type of expressions would be effective in stereoscopic 3D. We determined that looking down on a room from above would be a good match for 3D, and when we created a level in which Mario walks from room to room, we ended up saying, 'this seems oddly familiar… it's Zelda!" he added with a laugh. "Having taken things that far, we decided to add a number of ideas from Zelda. Since it was the 25th anniversary of Zelda, we could have made the Zelda tribute level 2-5, but we didn't think it would be a good idea to put the level in too early, so we made it level 5-2 instead."
On experimenting with Galaxy 2 on 3DS...
"When we started developing the game, we displayed Super Mario Galaxy 2 on a small TV monitor and found that Mario looked like a speck and that the game was difficult to play. This led us to look into the camera and terrain types that would be conducive to playing on a portable screen with a relatively large Mario. If we were making a console game, from the very start, we wouldn't have been thinking about any of those things, and I think the game would have probably been a lot different."
On the inclusion of the Boomerang suit...
"We created the Boomerang Suit after the boss character Pom Pom started throwing a boomerang. We thought that it would be interesting if the player could throw a boomerang too. There's a Hammer Mario in Super Mario Bros. 3, so one way of looking at it is that the thing that Mario throws has changed from a hammer to a boomerang."
On why the Tanooki Suit doesn't let you fly...
"The Tanooki Suit was introduced as a means of supplementing Mario's jump with the power to float. Many people asked us if we could make Mario fly, but when you can fly anywhere in a 3D space, a lot of problems come up."
On Kuribo's Boot being rejected for Galaxy...
"Our team always considers bringing back elements of past games. I myself proposed bringing back Kuribo's Shoe for Super Mario Galaxy, but tragically, my idea was rejected by the director, Mr. Koizumi."
On Super Mario 3D Land being the missing link in Mario games...
"We felt that there was something missing in the evolution of Mario gaming between Super Mario World and Super Mario 64. This feeling gave us the idea that we could create something interesting by applying 2D Mario rules to the 3D Mario know-how that we had accumulated."
On the return of end-level flags...
"the decision to return to the concept of flags sprung from the idea that if, instead of creating a game centered around searching we created a game in which players could always reach the goal by moving forward or to the right, the game would be easier for a wider variety of players to get into."