I kind of doubt they'll be doing one considering the Yoshi games haven't strayed from 2D in all the 15 years that the rest of the Mario franchise has been 3D, and newer Mario games are only feeling more and more like the 2D ones, both in that they brought back the Super Mario Bros. 3-esque gameplay with the New Super Mario Bros. games and in the sorts of gameplay mechanics being introduced into the 3D games, namely how each one is more linear than the last. I actually think it's pretty cool that the Yoshi games are gameplay-wise pretty much a direct continuation of the original 2D line, especially now that Nintendo sort of went back and branched off of SMB3 again with NSMB, resulting in sort of the NSMB branch and the SMW/Yoshi branch.
That said, your gameplay idea actually does sound pretty fun. A 3D environment would definitely allow more interesting egg physics, and with that more interesting egg puzzles. I'd like to see it as more of a physics game than as an old fashioned Mario-style platformer.