WCS changed the code to suit them and only them. I don't have a problem with them doing that, it was the whole reason they wanted to fork the code. But when we port stuff over to SCP we should do it in a way that makes the feature available to everybody, not just WCS.
I agree with Matth, we'll never get WCS to run on SCP as is. They introduced SEXPs that have no business being in the SCP codebase and will never be added (SEXPs which set or unset ship flags come with a host of annoying problems, which is why I introduced the alter-ship-flag SEXP). We'll need to make a new release in order to deal with that issue anyway so why no simply do that for all their changes? What we need to do, is to work on a version of WCS_Open which has as many of the original features added back in as possible.
In addition we should start working on putting back in the features that WCS didn't have but should. For instance multiplayer, from what I understand all WCSOpen needs for multi to work is the interface art. It probably needs its own process on FS2NetD eventually but that's not an enormous problem for now.
Matth, do you have a file describing exactly what you had to take out?