So far, the most annoying thing I'm finding (besides struggling through long eventing sessions, which are mostly my own doing) is the limit on "unique" character creation. And that, so far, I haven't found a way to add additional options (not even something basic - like, say, color gradients for hair instead of the basic 8 [i think] color options listed) even if I could find the resources.
As well, the ability to add facial expressions that won't look awkward (or in some cases, nightmare-inducing @__@) onto a single character's portrait sheet without needing to Photoshop/GIMP them together would help. I'm probably over-complicating the process, but I love being able to see when characters (at least the main ones) are angry without resorting to speech-bubbles all over the place. Even just trying to figure out how to make characters look happy/sad/angry/etc. is a task that (in my opinion) takes longer than it really should and can produce some... frightening results if misused. :\
Also, maybe it's just me, but the head-on portraits also looks... off. The wrong face makes them look like they're staring into my soul!
I know at the end of the day this is more of a gripe than a deal-breaker, that it might drive the price up a bit, and that it might be covered by DLC/add-ons (to an extent), but it would help make portrait creation more diverse.
*is grumpy ATM because there's no decent "Asian" look in VXA*