I wouldn't recommend generating PDFs because like you said, it will take a lot of time to generate the templates.
BUT: You can create HTML templates and have PHP parse it and insert the data. One good template parser I know of is called fasttemplates or something like that.
What kind of reports do you want to generate? If you want to generate graphs, use the GD library (as outlined by some articles here at phpBuilder).
-sridhar