While a lot has been written about this, I don't believe most people are actually aware how big a deal your site structure can be to your search engine rankings.
We recently saw Google go from indexing 100 to 450 pages of a website, overnight, because of a slight change in the site structure - which hardly anyone would even have noticed.
What was this about? A site search function linked to individual pages under many different URLs - plus it was turning out bad links in some cases.
The net result? The site was confusing to Google. Google thinks it will be confusing to the visitor and downgrades it. We found and fixed the error. Within days, Google showed its appreciation. Consider it a sigh of relief on behalf of site visitors.
Tools such as the "canonical tag" can help in an instance like this.
But many sites are built on funky Content Management Systems, or are built like a rabbit warren without any logic, rhyme or reason. They've long since outgrown the original planning and have had rooms, rooms and whole wings tacked on wherever they fit.
Don't think Google isn't aware of this.
Google is interested to serve up the most relevant results for searches. The larger the site, the more likely your site will have what they are looking for. But, also, the more confusing the site, the less likely people will find it.
Many times there is no cure but rebuilding the entire site on a better platform and with a structure thought out from the beginning and that makes more sense.
Help Google Help You.