It will not install on some commercial web servers - If you are planning to use it on a commercial host check with them 1st and save your self some trouble (godaddy shared hosting - forget about it)
The application is quite complicated and not for the faint of heart. If you have a problem digging into php and mysql this is likely not the application for you.
One other thing the developer community is very unabashedly bias toward "another cms" so keep that in mind while looking for support
While this is the right application for many organizations and has a great feature set be forewarned is is a bear to administer.
Would be good to get more details on:
1. "The database structure is a total mess." A complex db structure does not necessarily mean its a mess.
2. Depending on your application, mysql has got quite a few backup utilities which can safely backup a running mysql instance
3. "the developer community is very unabashedly bias towards 'another CMS'". So does this affect the support that is offered? if so, any examples where this is biased
4. We pretty much are upfront and do warn folks that cheap shared hosting services (goDaddy, site5 etc) are not a appropriate match for CiviCRM