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Most cases like these are catered for on an adhoc basis, usually done by a dev team that will migrate the entire database into the new site. There could well be a market for a porting tool that provides a checklist type system for a large scale site migration. I have seen site migrations go wrong. A lot of revenue can be lost through the plummet of organic traffic from a failed migration.

Uglier  URLs is not the end of the world, I personally was able to rank clients websites with very ugly URL like, site.com/238313 However once your new site is under development why don't take the time and implement the clean url? I'm a sure a clean url will help with SEO and also is much better for usability.