My gripe with the Creation Kit was that ultimately it all boiled down to Actor Values (skills, elements, resistances) - which were hardcoded. So my first mod, the School of Magic of Darkness, never worked because of that. So, want to create a new element? nope. Want to create a new skill tree? Nope, not without overwriting others. All existing ones are replacers, workarounds are ok but still. Plenty of room for worldbuilding and adventures, however.
I see what you mean. Construction Set gave a lot of flexibility even without the 3D modelling but stuff like that was extremely irritating. Even as a modeller rather than a storyteller it was incredibly irritating as it made random stuff like adding facial hair, jewellery etc (which was actually very straightforward in terms of how it could be rendered) tedious bordering impossible because of the extremely rigid slotting system. And that was just aesthetics. Must be even more annoying regarding the other stuff. Plus the problem that there were so many bugs outside of what you might expect from random scripting errors.
But as a Bioware fan where the scope for modding is practically non-existent, especially with the ME games, I guess I still feel grateful for what I can get... even if it could be so much more. Which is why I'm nervous about Bethsoft ever updating its creaky old engine as who knows what the future may hold, especially after their foray into online gaming. But given that their release schedule has become so tardy, maybe it's not that important any more. That said, I've wandered completely off-topic there. :o I'm not sure what the best way to deal with it as at some point they (as in games devs in general) have to draw a line with what can reasonably be customised.
But even when it can reasonably be customised, I just wish there were more open standards so that it wasn't down to particularly dedicated modders to reverse-engineer e.g. the GR2 format du jour and numerous other examples of the same.