Site architecture analysis includes:
Check if social media profiles exist, make a note of fans and followers.
domain redirections
Preferred domain setting
Checking internal links for inconsistencies
Domain blacklist checks
Domain hijacking issues
Checking sitelinksWeb crawl error reporting
HTTPS issues
URL structures
URL deep directory depth issues
URL separators analysis
URL capitalizations
HTML and XML sitemap issues, sitemap listed in robots.txt or not
robots.txt issues
CSS/JavaScript issues
Background Images issues
Broken links check
Meta tags analysis (title, header tags, keywords and description)
site speed issues
SSL issues if applicable
Session ID issues
Source code size issues
User download size issues
Breadcrumbs issues
ViewState code issues
NoScript code issues
Custom error page issues
User agent and cookie checking