I could be wrong, it has already been mentioned that we cannot read the minds of the devs, but I'd be surprised if performance was a huge consideration for the disappearing corpses. The reason I say that is we are not talking about that many corpses and, by the time Strife came out, the base-line for computer performance had increased over what was available when Doom came out - which could have just as many corpses. Mind you, Hexen has its corpse queue, so maybe.
It could well be a style choice for the reasons that Crowley suggested and, at the time, it wasn't unusual to have games where the corpses faded/ disappeared (in fact, it is still common), so the corpses fading in front of the player wouldn't be that unusual. The mere fact that they go to a gib frame before disappearing shows that the devs had considered the player seeing the corpse vanish. Against that, however, is the fact players being familiar with corpse vanishing in games
was primarily driven by performance issues in the first place. I do remember a friend of mine making a comment back in '94 about how cool it was in Doom that the bodies didn't disappear.
Regardless of the devs reasons for doing it, the decision does seem like it was a last minute one, with a rushed implementation demonstrated by the map-placed corpses vanishing (something that I confess that I had never noticed). Personally, I prefer the corpses to remain. IMO, it looks better and, as PDF said, they act as a marker for areas that you have already visited.
Aesthetically, and logically, I can accept corpses lying around in strife. This is not a functional society. Despite the way "The Order" seem to be ruling the planet, I can accept that in the crazy, mixed up, post-comet world that bodies would just be left to moulder in the streets. Conversely, I can also accept that corpses from the likes of the acolytes might fade away and vanish due to accelerated rotting because of them effectively being a sort of host for part of the alien consciousness. However, the clumsy implementation of the "feature" implies that either a mistake was made with other corpses or that it was not the intention to imply anything about the nature of the acolytes by the corpse fading.
Bottom line, I prefer permanent corpses.
