mystcraft isn't currently on mindcrack, so for the people most concerned about balance it's a non-issue. All of thaumcrafts transmutes incur loss that I can tell and compared to other mods a lot of items are really lacklustre, not seeing the problem there. Soul-shards is ridiculously OP even without the soulstealer enchant.
I agree about TC the dev has gone a long way to keep it from becoming easy to automate. Which I like as a said else where TC's transmutations are basically more a "Oh I need some of this now" and less a "Ok lets plate a starship in gold and call in the Blingstar". TC is powerful but requires a time investment both for research and for actual use. What automation is has is good but vary little of it is self automation.
But I'm on the fence with soul-shards. I like them and I think they would be really easy to fix by removing or nerfing the ability to steel from in world spawners. I spent a little over a (real world) day and a half getting the 8 I'm currently using. And time to get tier 5 was Night and Day different between the ones I could get spawners for and the ones without even with soul stealing. If I could find spawners (blaze, skeleton, zombie ect...) it would take me about an hour to get to tier 5. If I could not but I could build a spawn room (enderman, pigmen, ect) it took about two or three hours. But if I had to hunt stuff down (passive mobs) it took hours and hours. Yes the finaly product it awesome but my unlimited wool from my sheep soulshard took literally like five hours to get and compare that to a normal sheep farm setup I probably could get the same effect for much less time. Also I look at most of the other mobs and feel it is not to OP because you can always just build an old style spawn system and get vary similar outputs. The ones I think are sort of OP are the blaze and Wither Skeletons only because of the product for power use. But even toughs are not to OP because lets be honest a blaze farm in the neither is child's work and about an hour.
So yeah I can see your point about the shards being a little powerful but I would not call them ridiculously powerful. And I honestly think just editing the config to give you 0 instead of 200 per spawner fixes any OPness in the mod.