The trouble with Wing Commander is that the series is built a bit too much on its presentation, the first two are the ones that aged the worst, the third is fine but repetitive, the fourth is the best of the series being the most lavishly produced and the least repetitive (also it has more branching paths in its story, you can totally be the bad guy with the right choices) while Prophecy tends to be more on the level of 3 though it has its moments here and there.
Unfortunately the trouble is that apart from IV (and to a lesser extent Prophecy) very little of the story is told during the gameplay, almost nothing in fact, secret ops is particularly guilty of this, doubly so since it came after IV.
Also while from 3 onwards the games try to incorporate some of the innovations introduced by X-wing they tend always to be lousily implemented, for example the energy distribution controls are lousy in 3 and 4 and only get worse in prophecy for some reason compared to the ones in basically any other space sim.
Prophecy has the same problem of three with throwing wave after wave of fighters at you only worse, with the added annoyance of spongy enemies that abuse the afterburner like there is no tomorrow, I even ran out of afterburner fuel a couple of times which for me was a first in the entire series.