I'd like to add a thought about stability. Remember that many shops consciously stay a revision behind on Drupal releases (at least for 6 months). This is because of the myriad of necessary contrib modules (like views etc.) that can take a while to get ported and become stable. And also, it usually takes Drupal a month or two to get to a truly stable release (ala 6.2). Stability is key for existing shops, especially with requirements like PCI and third party integration with things like PayPal etc.

So, I'd like to suggest that porting without radical changes is usually the best approach. It reduces the "moving target" effect of testing things that are broken, things that worked on a previous version and are broken in the newer Drupal version. Keeping adjacent releases (5.x 1.0, 6.x, 1.0) in sync will make testing and maintaining stability much easier. And if bugs appear in new versions, you can look to the differences between Drupal versions and not worry about changes from a radically reworked code base. This issue will surface again when you abandon Drupal 5.x and are porting 6.x to 7.x. If it's good enough to be 1.0 on 5.x, a direct port to 6.x should be a good 1.0 as well.

I feel that a major reworking should be done as a Uber 2.0 release, and probably for Drupal 6 or 7 only. I'm wildly guessing that porting the existing structure to Drupal 6 will not take as long as doing a rework and port. This will also allow you to get a 6.x version out the door and take your time with a 2.0 rework -- which will always take much longer than expected. The automatic doubling rule usually applies.

Ok, not trying to preach, just my two cents from running some rather large projects over the years and trying to keep up with moving targets. Whatever the outcome, I truly appreciate your efforts and hope to start contributing code/patches to the 6.x effort.