My guess is cutting out on Wither farming. With T5 Wither Skelly spawner, you start swimming in skulls, so you can farm Wither over and over to get Nether Stars, which many mods use as an expensive component for balance reasons. Without the skull drop from wither skelly spawners, you're forced to hunt Withers in the Nether, build a vanilla mob trap for Wither Skeletons on the Nether (Which is kind of very tricky to do), or use a portal gun to transport vanilla skeleton Spawners to the Nether, since those will spawn Wither Skeletons on the nether, and build a trap like that.
So basically the only thing that changes is now you don't build a T5 Wither Skeleton Spawner, you instead procure Lots and Lots of skeleton spawners from TC barrows in the overworld/mystcraft ages, build a trap in the Nether, and nothing has changed, except the author of Soul Shards now has a clear conscience in that his mod cannot be use for infinite Nether Stars. And you're more or less annoyed because the vanilla spawners will only work if you're in a 16 block radius from it, so you'll have to stand in the Nether doing basically nothing until you amass a sufficient amount of Wither Skeleton skulls. Or you go do it the Hard way, and build a vanilla mob trap in the Nether, for Wither Skeletons. KaboPC has a good tutorial on how to do it the most efficient way, and even get a mob separator going on that puts Blazes on one side and Pigmen/Wither Skellys on the other side. Any way you choose to go about it, you'll now have to BE in the Nether in order to farm your skulls.
For me? I *kinda* understand the reasoning that went behind this decision, but i don't think that it makes too much of a difference in the end, since other than making the player resort to more time consuming and less efficient methods that achieve the same end result, it doesn't actually change anything in the meta game, which i believe was the authors intention (Make Soul Shards play nicer with other mods that use Nether Stars in their more expensive recipes). In fact, for experienced mob trap builders, it may be possible that building the trap in the nether is actually faster, if more resource consuming(Pistons, redstone), than killing the required number of wither skeletons. Clearing the terrain around the spawner to make it so that no mobs spawn anywhere else other than the designated mob grinder is made trivial with Fillers, a process which normally takes ages in vanilla minecraft.
