With how optional flying and using the special capabilities of the Yoshi's were, I really don't see how either is much of a problem. You could play through this game nearly from end to end with ease and just utilize the standard capabilities you've had since the first Super Mario Brothers. I can't think of any areas that required you to fly and only one area in the Special World where I believe you all but need the blue Yoshi's flying capabilities to reach the goal.
And it's not like you'd ever be specifically be seeking out a yellow Yoshi (Creates a small earthquake after eating any colored Koopa shell)) or red Yoshi (Shoots fireballs after eating any colored Koopa shell).
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