Two of my (sucessful) Systems Engineering MSc students had this to say about system development projects, from different angles:
The architecture of a system and the organisation of that work are fundamentally interdependant.
Well, duur. Aside from the obvious, we spoke at length about the two sub-systems: the product side and the project side. Like all systems, you don't want to optimise any one part, but the whole.
Here's another case: software (specfically, database) development at Flickr (a burgeoning product, with a comparatively tiny dev-team). Sometimes the usual quality criteria on the product side may be better compromised if you want to achieve desirable behaviours on the project side. Ergo, by way of interconnected, don't bother normalising your data tables like you were told in college.