Mine are fairly minor, and in no way deter me from wanting this baby.
- I don't like that the door covering the optical bays has it's hinges on the same side as the window. Obviously most people will position the case so they can see their gear through the window, so the door swings the "wrong" way.
Pretty common complaint and I agree. For some reason many are this way. 
- I'd like if the panel with the Phanteks logo on it had a smaller removeable panel - take out the HDD cage(s) and that'd be a great location to show off a pump/res combo unit, especially given the stylish small window on the side panel.
That's a great idea!
- The bracket at the right of the mobo tray could have been thought out a little better - two or more of the longer graphics cards means the whole thing has to be removed I think?
Not sure what all can be done to deal with this issue. Maybe make it a 2 piece bracket with different covers.
- Front dust filter is screwed into the front panel - seems overly cumbersome for cleaning purposes.
Dust filter is held on with screws and clips. Removed the screws and clips hold the filter nicely.
- Not a fan of blue LEDs
I'll have to mod the strips at the front and top of the case.
Jesse on TheModZoo changed his blue LEDs to white. http://themodzoo.com/forum/index.php?/topic/883-enthoo-primo-front-led-color-change/
As I say, all fairly minor points and most can be fixed with modding.