If your site is brand new, has no backlinks, and/or isn’t getting any traffic from search engines, there is really no need to worry about the redesign effecting your rankings–just go for it. If, on the other hand, your website is not in that situation, these are the things to pay close attention to from an SEO perspective.
URLs
Changing a URL without implementing a 301 redirect from the old URL to the new one will wreak havoc on your rankings.
Content
The changing of content on individual pages can have a big impact. Even if you don’t change the wording, the CMS may place content elements in different locations within the HTML, causing search engines to understand the importance of some aspects of your content differently from the old page to the new page.
Internal Linking
Changes in how internal linking between pages is accomplished can have a huge impact on rankings for your pages. External backlinks to a page aren’t the only thing that help a page rank well–backlinks to a page from within the same site also count. Remember, when you are looking at a web page’s HTML, only the first link to a specific page from that HTML can count as a ranking factor. If, in your redesign, you move to or add JS, image, or flash links, you can adversely impact rankings.
Duplicate Content Due To URLs Created By CMS Or Ecommerce Platform
You may also find, due to the way your CMS creates URLs, that you end up with duplicate content issues on the new site that you didn’t have on your previous site. Duplicate content is the exact (or mostly exact) same content found on different URLs and it is typically a negative when it comes to SEO.
Navigation
Changes to primary and secondary navigation can have a huge impact if not looked at closely from an SEO perspective. Will the new site be using CSS, JS, images, or flash? What was the old site using?
So, there you have it. For several reasons, changing CMS’s can have a big impact on your site’s rankings and Joomla CMS fresh out of the box (un-tweaked and un-refined by you or your SEO) is not going to deal with these issues as well as you hope.
