The Theme system in Drupal is existing and working very well. A database abstraction layer is in work for the coming version 7 - in case you ever need one.

You failed using Drupal because you probably did not take the time to learn what Drupal really is. It's a framework, not a CMS. Though it includes CMS-like functionallity on basic level. Learning it takes some time not everyone can or want to spend for.

Using the Drupal API you are able to implement business logic as in any other way - just faster and in a clear manner (as it is true for most frameworks once you know them).

Writing your own code (probably poorly tested/documented because development itself took most of the budget) sounds like the World of Frameworks aka helpful functions did not touch you yet.