ZDoom

On top of that, how many replacement actors follow the pattern of "actor [i]x[/i] : [i]y[/i] replaces [i]y[/i]"? If [i]y[/i] is just a dummy definition, it's still going to be broken.

I guess a "replaces optional" thing could be added for such non-critical actors added by another port or mod or whatever, but how long would you have to wait before the relevant port updates to recognize the new keyword?

The only way that won't cause problems is to duplicate the editor numbers and live with the warnings in Skulltag.
Everything else is just introducing needless stability issues.

The thing is that, unless you put Skulltag and ZDoom both in the same directory [i]and[/i] use the hacky Skins folder method to autoload files, what is autoloaded by ZDoom and what is autoloaded by Skulltag are separate lists. One is in zdoom-user.ini, the other in skulltag-user.ini.

There's really not an elegant solution to this either way -- that method would throw up warnings in Skulltag, while trying to use thing # replacement (which is deprecated and not recommended anyway) will cause trouble as well.

Wouldn't adding such dummy definitions to a pWad cause them to replace Skulltag's actors anyway, since skulltag.pk3/wad is loaded first?

No, it hasn't. But if these actors are defined in a broken way in ZDoom other mods would suffer. In that case you are better off making your own dummy definitions and autoloading them instead of adding some useless crud to zdoom.pk3.

It's not possible to load Skulltag mods in ZDoom if the 'replaces' keyword is used to replace a Skulltag actor, unless that has been changed recently.

That doesn't sound like a smart idea. Since it is perfectly doable to load a Skulltag features add-on with ZDoom, such mods would suffer from it - and I won't do that.

ACTOR <CLASS NAME> <DOOMED NUMBER>
{
}

Since you can't replace classes that don't exist, would it be possible to add "empty" decorate definitions for some of Skulltag's actors? Like so:
[code]
ACTOR <CLASS NAME> <DOOMED NUMBER>
{
}
[/code]
This way, it's possible to replace Skulltag actors with new ones without breaking compatibility on (G)Zdoom. It would be much cleaner than having an extra wad/pk3/whatever to fix any errors that come up from replacing non-existent actors, or adding an empty definition into the modder's decorate. They would still have to define the entire actor again, but they would have to do that anyways if they were trying for compatibility.