The MD one isn't perfect either. It has its own batch of issues, like no continues, details missing, as does the Genesis one (even less voice content and too easy, along with said graphical details missing that are gone on the MD version).
Two exclusive PCE stages in Strider! No, they aren't amazing, but it's interesting to see how PCE version could (and should) have been SO MUCH MORE BETTERS than the actual game we got.
I've never played this game and was in chat talking to a few other people about it. lukester said there is actually only one exclusive level in the PCE port. He also mentioned the Genesis version is harder than the PCE counterpart but he never really mentioned why though *shrugs*
The Genesis version is the easiest of the three. Its difficulty was watered down drastically from the Mega Driver version to such a degree that to match it you have to go into the options and set it to hard to equal the normal mode of the MD and PCE ports. The content exclusive to the PCE is the extra desert stage, cd soundtrack, and somewhat animated cut scenes that were extended somewhat to provide a more detailed story.
Also worth mentioning, Grandmaster is missing the digitized speech near the end on the Genesis, and Hiryu is silent during his attacks on the Genesis port. Basically if you want the best versions, its the MD and PCE one.