The type of class to use is the subject of some controversy among R programmers. In essence, your view here will likely depend on your personal choice of which you value more—the convenience of S3 or the safety of S4.
John Chambers, the creator of the S language and one of the central developers of R, recommends S4 over S3 in his book Software for Data Analysis (Springer, 2008). He argues that S4 is needed in order to write “clear and reliable software.” On the other hand, he notes that S3 remains quite popular.
Google’s R Style Guide, which you can find at http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html, is interesting in this regard. Google comes down squarely on the S3 side, stating “avoid S4 objects and methods when possible.” (Of course, it’s also interesting that Google even has an R style guide in the first place!)
A nice, concrete comparison of the two methods is given in Thomas Lumley’s “Programmer’s Niche: A Simple Class, in S3 and S4,” R News, April 1, 2004, pp. 33–36.