The idea with the catalog structure is GREAT for huge sites. i really like it, i have seen tons of cms's but this one has its benefits.
The no:1 thing i like is search engines find the sites much easier and i can get more sites indexed.
This is very good, and i intend to start using drupal for my site, and possibly in my work, if some steps are made in the new version.
Drupal has a few wrongs in it, I will give you some very good tips to put into the new version, and hopefully you will do the following steps, cause it will increase traffic and search engine placement for all drupal sites.
It's not how many sites google indexes, its how high up you get them.
These rules apply to some other large search engines aswell.
1) google does not index more than 1 id. (this is eliminated with he catalog structure, wich is good :) )
2) on drupal, you do not have different titles for different sites...
Lets say we have a site named "Drupal | community plumbing"
like this one, but we go into someones discussion, lets say this one, on a search engine optimised site... the title would now be "Drupal | Search engine tips for drepal.org development"
If you have the same title on 10000 pages, and similar content in like 4000 of them, google will not index them, cause it thinks it is the same site.
3) Just a little note for you writers out there, the titles and desciption of your articles, tutorials, or whatever your site contains, dunt make them too large, if they are too big google will skip them.