Search engine robots are the automated programs that scan the text, read the tags and navigate the links present on a website and then index it according to it's fixed algorithm. So, plain and simple, ease of navigation and quality content are the key constants in the search engine optimization process. Complicated or complex website design may confuse the search engines robot, an action that is not desirable if you want a website that gets results.
Although you may have a complex website with exceptional design and features such as frames, Flash, java script, mouse-over links and graphics. You simply need to contact a website design company that understands how to intract with search engines with these features and get design the website in an optimal manner.