Thanks for writing back, I appreciate it. Please know that none of this is personal - it's about the code, not about the people writing it.
I very much understand the process you're going through. I'm one of the lead developers of WP e-Commerce - have been since 2010. That plugin has been around since 2006 - so I know exactly the pain points you're imagining, the pros and cons you're balancing, the weight of a large project, etc. I get it. We have over 2.2 million downloads - I understand the weight of code + community ;)
Beyond that, I was the primary developer tasked with converting the admin area to utilizing custom post types for everything - we had custom tables for products, product categories, variations, etc. It's all custom post types and taxonomies now. So rather that use the cop-out that "it's not fair to evaluate the quality of the code" - let's take some personal responsibility here, recognize that proper code is worth evaluating - and move forward. Saying that it's hard to change a major code base with lots of customers - that's true, but it's just an excuse - not a valid reason for not doing it.
And I'm the last to point the finger and call something garbage without good reason. Have you seen some of the reviews against WPeC? I've been on the receiving end of that enough times to know better. That said, certainly you know as well as I do that it's beyond silly that here we are, in 2013, and you have custom tables for categories, pages and ads. Right?
So, that all said - write your upgrade routines, move to custom post types and taxonomies, don't break backwards compatibility - a tall order, but our history testifies to the feasibility - and I'll happily change my rating. I should imagine you'd shave off thousands of lines of code, as we did - and have a much more performant and maintainable plugin.