The trophies that will be offered in the upcoming Super Smash Bros. for 3DS can be purchased, director Masuhiro Sakurai said on Miiverse recently, and a screenshot he included indicates they may be purchased with the handheld's Play Coins.
If so, that means players who are having a hard time collecting a rare trophy could add it to their collection simply by taking a long (probably very long) walk. Play Coins accrue when you carry around a 3DS in sleep mode.
Trophies in the 3DS edition will be different from the Wii U version.
The trophies also can be purchased with Super Smash Bros. in-game currency, and Sakurai said some will periodically be placed "on sale."