Lack of dimensional accuracy is my main complaint about it. I'm often wanting to mate up 3D printed plastic parts with machined parts, and the different materials all have different tolerances and shrinkage rates. From what I can gather, they also don't shrink uniformly; it varies based on thickness and surrounding material, etc. I need to practice more with different materials to get a feel for how they shrink and how much I need to offset for that when designing parts.
I was very happy with the 3D printed drop-in part for my Tuvok lamp, though. It allowed me to get a part that perfectly conformed to a screen-traced profile that would otherwise have been really hard for me to turn on the lathe manually.
It wasn't a tight-tolerance mating of the two parts, though. I just designed it with a fairly big overhang over the hole I dropped it into and that was that.
The main reason I'm really into 3D printing right now is how easily it allows me to play with things digitally before having to worry about the actual manufacturing process. Up until very recently, everything I ever made was some kind of digital product, from design, to writing, to software, so I'm used to low-cost iterations in a sort of abstract Platonic vacuum. I can sit at my desk and design and re-design parts in CAD software all day, but when I'm standing at the milling machine and break a $50 end mill because I accidentally set my feed rate too high, I succumb to despair very quickly and get frustrated. CAD is great because it lets me catch my errors by playing around with the parts before committing to anything real. I can fiddle and finesse and obsess (as I am wont to do) without incurring any major costs beyond lost time.
So I guess what I'm saying more than anything is that I like 3D CAD, whether the ultimate destination is a 3D print or a set of machining processes. Eventually, I dream of getting my own home workshop with a good 3-axis CNC machine where going from a 3D model to a part is almost as easy as 3D printing, but right now 3D printing is just a much easier from getting from a CAD model to a real-world design.
But for anything other than really small parts, 3D it gets expensive really quickly. For example, I designed a little tool holder the other day for holding the nice set of sculpting tools I recently bought. I wanted a master in plastic from which I would then make a mold and cast it in concrete.
Even though the walls were very thin...
Shapeways wanted $800 (!) to print it because of the machine space it would take up (it is about 30cm, I think). Whereas I could probably hire a machinist to make this for me for a tiny fraction of that price.