Hey There,
I personally believe that given you take the correct measures to make your system “SEO friendly” you will only gain from using CMS.
Let’s review the “Downsides”:
1) Non SEO friendly URL’s – search engines generally dislike parameters such as ?pid=DSDA&sid=dsdasda. Can be solved using “MOD Rewrites” which make the “front” layer URLS anything you want them to be from .html, .PHP or without a suffix at all if you want. You can also sprinkle your keywords and category names in there, for example xxxhttp://www.whichpoker.com/beginners-guide/poker-rules is a CMS based site with “friendly” url’s.
2)
Design restrictions – Using a generic system such as wordpress, Joomla, PHPnuke will save you time but will generally define the way your site will look. As you have probably seen most wordpress sites like rather similar and are usually simple 2-3 column designs.
Customization of different page elements takes time and programming knowledge. By elements I mean lists, changing images, Meta Data in the CMS and more.
For most newbie’s using a “generic look” site and CMS is not a big problem and I can assure you from my experience you can reach good rankings anyway.
The best way to customize AND use a CMS is building a customer made CMS to fit your designs. This is the only way we work with all our sites (you can use PHP, ASP, Java, CFM or any other server side language for this), problem is this takes time and money.
3) Security – Many CMS’s have some security hazards and “cracks”. I think that using an open source popular CMS will help you avoid this and keep you in the loop of security updates, frequent new plug ins and so on.
4) Directories, not a problem in a custom made CMS as you can make which ever tiers you want. (Bodog.com is a great example of this using JSP) , in simpler CMS’s you can also, WordPress allows you to create as many layers as you want and so do Drupal and some more.
To summarize, In my opinion CMS is the only way to go. The advantages of having an easily updateable site overcome all possibly disadvantages.
As for either going the custom made route or generic it really depends on your resources, budget and time frame. More details about your background and what you have in mind will make a recommendation easier.