First time doing this. I haven't played many "Yoshi" games, but I'm going to try my best.
Love Is In the Air/Tall Tower - Yoshi's Story - N64 - 1997
I believe that including the main theme of the area the stage is based on is standard when it comes to stage music selection. The two themes would alternate after playing their respective variation of the main theme once.
The Riddle - Yoshi's Story - N64 - 1997
While Baby Bowser's Lullaby is more iconic, this variation of the theme, in my opinion would fit the stage better.
Title Theme - Super Mario World 2: Yoshi's Island (Arrangement in link comes from Fortune Street) - SNES/SFC - 1995
A notably under-used track in the series that I feel would fit with the stage. (Although it would be a different variation of the theme.)
Underground Theme - Super Mario World 2: Yoshi's Island - SNES/SFC - 1995
An iconic track in the series, another that would need a remix.
In the Clouds - Yoshi's Island DS - DS - 2006
While overall the same melody as the Wildlands theme that's already in Smash 4, this variation of the theme has a different feel that still fits with the stage.
Hotfoot Hurdle - Yoshi's New Island - 3DS - 2014
One of the few songs anyone likes from the game. I'm aware of the unpopularity of the game in general, but I feel it's relevant enough to use another variation of the theme.
Theme C - Yoshi - NES - 1992
An obscure track, and I'll admit that I find it strange that the game is in the "Masterpieces" section of the game when there aren't any elements from the actual game. (Another track that would need a remix.)
Boss Battle - Mario & Luigi: Partners in Time - DS - 2005
As Swampasaur said, since music from various Mario RPGs appear on Woolly World, this song should be OK here. Also, this song (or some other song from the game) was supposedly going to be in Brawl and since this game features the Baby Mario Bros., who are a big part of the Yoshi series, also appear here, it fits slightly more.