Making and keeping all the slides looking consistent is taking forever. Every time you have to change something, you have to go back and change every slide by hand.
What's worse is, when the overall look of the presentation needs to change, you have to go into all of the other PowerPoint files in this project and make the changes by hand.
Every presentation should be based on a template. If you keep the templates clean and usable, changing the look of presentations will be much easier. In addition, the more of the design work kept on the master slides, the easier it will be to make presentation-specific changes.
In PowerPoint 2002 or later, take advantage of the multiple masters feature. If you need to have some slides follow the same pattern as the rest, but with a certain element always in the same place, make a master just for that series of slides. Changing the slides will become much easier.