As search marketers, it's our job to know the makings of a well-optimised site and get our clients to implement those as best they can. In an ideal world, all the SEO best practices would be implemented at ground level, at the time the website is being designed. This would give the freshly launched site a better chance of being indexed quickly and remaining competitive in its niche. Of course, this hardly ever happens. Usually, a company would have a website built and launched and then turn to an SEO to help promote it. By the time I, as a search marketing consultant, get approached, it's usually a matter of dealing with an established site that has been built to entirely different specifications than the ones I would have given as an SEO professional. The pages of such a site could already have been indexed by the search engines. They could be appearing in the SERPs in response to various queries. In the case of some sites, there could even be quite a well-established presence to contend with.
It's tempting to look at a website, see the elements of it that don't conform to the "rules" and decide to make drastic changes in order to make it comply. I must admit that when I started out as an SEO, I nearly fell into that trap myself. Luckily, the developers whose job it would have been to make the complicated, time-consuming changes I suggested were not so keen on doing the work without apt justification. This forced me to do some more research, at which point I discovered things are not always as clear-cut as they ought to be.
The fact of the matter is that you can't simply SEO an established site by the numbers. You need to examine it carefully first to see which parts work and which don't. Rather than force compliance at all cost, your goal should be to work with what is already there. By all means, change the under-performing parts but leave or strengthen the parts that work well, even if you think that, by right, they shouldn't be doing as well as they are.
Take as an example the matter of URLs. The general consensus is that keyword-rich, short URLs are better than long, convoluted dynamically generated URLs. Mod rewrites, redirects, etc. are all commonly used by webmasters in order to make their URLs more search engine friendly. But if a page is already indexed and is ranking well with its dynamically generated URL, is there really an urgent need to put time and effort into changing it? After all, you could be causing more harm than good by messing with a winning formula.
Pages with dynamic URLs may be less attractive to search engines, but in reality they can still get indexed quite happily if they conform to other SEO rules (like have links pointed at them), at which point their less-than-ideal URLs become less of an issue and your time could be better spent fixing actual problems.
The WWW and the search landscape in particular are constantly changing. The search engines are continuously working on improving the way they access and archive information and things that used to cause them problems in the past may have become easier to deal with. So before you decide on massive, sweeping changes, it helps to make sure they are really necessary and arranging your priorities accordingly.