What parameters to look at when comparing capacitors of same value but different package size
What gives? Cost, availability are non-technical factors. The smaller ones cost about triple the price in 1000's. You can check and see what other sources you have available if the TDK ones are not in stock. 

The voltage coefficient also tends to be higher for smaller parts, meaning you'll typically see less capacitance at operating voltage for the smaller part. 

Edit: You'll have to dig pretty deep to find the voltage coefficient specifications, on the manufacturer's websites. Here's some representative performance of similar Japanese-made parts (Murata), thanks to a Maxim article. 



Edit2: I really suggest you go to http://www2.tdk.co.jp/ccv/step3.asp. It's an online tool that will show you the typical characteristics of a TDK component directly from the part number. Most of the characteristics of the smaller part are worse including tempco and voltage coefficient (the 0603 almost does a disappearing act at 10V bias).




For what it's worth, I went through this selection process a few weeks ago and chose 0805 parts for two new products.