Well, Din's Flare (Fast Din's) and both Phantoms are just as useable as their regular counterparts, but won't make a big play style difference. (As theses move aren't to be used too often anyways. xD ) Just preference over certain aspects such as a very fast Phantom charge with lower angle but no distance or KO power, or a high shield damage but less power Phantom.
The rest aren't really viable tho, and you're better off using the normal versions in those cases. Not that they can't have fun gimmick uses, such as Farore's Windfall being lolzy way to surprise gimp your opponent as shown by (I think) D3RK.
I'd say Farore's Squall, and Nayru's (Both alts) are the particularly "don't use" ones. Just my opinion on that, though.
Squall is like returning to Brawl level startup, losing any invisible travel advantage you had, AND no damage or KO power at all.
Nayru's Rejection causes turnaround, but...That's it. Worse reflect frames, roughly the same end lag, way worse KB (Which is neat for a GTFO like Nayru can be.)
With Nayru's Passion, you lose the invincibility AND reflection ability, and get a small sized explosion that can't even KO till 170%. Not to mention the hit-box happens like, 30 frames in...LOL. The only bonus is it's lower than average set angle of 30 ish.
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RyokoYaksa says it well about why Phantom strike (the no distance one.) is useable.