My observation: It's simply not possible to fit all high quality parts and discrete components into an integrated. Take for example high quality capacitors which alone take a lot of space. In separates, you'd be able to use all the big caps you want, but in an integrated you'll probably have to settle with electrolytics in a lot of areas. My c-j phono stage does not have a single electrolytic capacitor, not even in the power supply; this design will not fit into an integrated.
Are integrated amps technically better than separates?
I'm assuming we are talking same class of amplifier and the integrated has the features you want. I'm thinking the integrated could actually be an improvement over separates due to being a more "direct" connection. Taking away the flexibility factor of separates, is my line of thinking correct?