It matters if you are trying to be undetected. You must keep out of sight, to remain hidden. With Fleeting Ghost, if you walk through the line of sight of a guard during your movement, he will see you. With Shadow Stride, as long as you are moving from cover to cover, the guard will not see you even if your movement passes through his line of sight. Speedy elves are truely masters of the Shadow Stride, sneaking into places right in front of a guard's nose.
Another big difference could be opportunity attacks. If you are passing by an opponent with Fleeting Ghost, you are not hidden, and will be subject to an opportunity attack. Shadow Stride may allow you to avoid being seen.
Strictly speaking, Shadow Stride is not exactly an upgrade on Fleeting Ghost, since it has the requirement that you must be hiding to use it, whereas with Fleeting Ghost, you don't have to be. But I'd say it would still be a good idea to train out Fleeting Ghost for something else once you get Shadow Stride.