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I would say that you should make sure that you don't have any orphaned pages. What I mean is if they are static html pages you need to remove the old pages from your server.
The most important question is: Does the new script make the users experience better?
If it does than it is always the better decision because if people enjoy the new software it will begin gaining backlinks even quicker
If your home page has let's say a PR3 normally your second level pages will be given a pr2 if they are indexed now, have age, and SE friendly URLs.
Your new pages will start with a PR of 0 but the home page. Google webmaster tools now gives you the option to remove old content from it's indexing and you can quicly help get the new content added by using an XML sitemap on google and yahoo.
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