I don't like the idea that dependencies are not handled in a unified way. By that I mean that both module.inc and update.php code is written to handle module status. There should be a central library handling their dependencies. When we handle this in a unified way installing a big project like ubercart is easy.

When installing/enabling a module it is important to know what this module is dependent of. Ie uc_cart is dependent of uc_order. See ie http://build2be.com/sites/build2be.com/files/ubercart.neato.png