1) Too many compromises - As beautiful and capable as the rMBP is, this is probably the least versatile 15" MBP Apple has made due to the lack of storage/memory options. (Mine works amazing for my photo work, but I cant make it also a gaming/entertainment machine or load it with videos due to lack of internal space)
2) Port Options - 2TB, 1HDMI, 2USB but no FW or Ethernet. The reason Im critical of the port choices is because TB hasnt seemed to become anywhere near standard due to lack of available hardware and ridiculous pricing. I wouldnt mind making this also a game machine but with only 2 USB ports then its tough because Headphone/Control Pad/Ext USB Drive = 3USB.
3) Gimmick - Im going to offend people by saying this but I do photo work on this and while I absolutely love the screen, Retina is a gimmick that not everyone needs. IF Retina was standard then thats amazing, but Retina comes at a cost since the cMBP that can do everything the rMBP can do but is cheaper and upgradability makes it a better in the longrun.
4) Resale - Ive been looking at Retinas used market for a while and in its short existence then the resale value seems to have a much higher dropoff than other MacBooks. So it would seem that in 2 or 3 years when Gen 3 MBPs are standard with 16GB/1TBSSD, the value of a 8GB/256GB machine will be pretty low.
Im not shooting down the rMBP. Its a good machine but IMO its not the flagship that it could've been and thats a shame.