How can you brand MySites in SharePoint 2010 so that all the pages look the same, including personal sites the users create? Changing 'mysite.master' only has an effect on some of the pages, not the 'my content' one (since it is under a managed path), so how can you update those sites, would have you to delete all personal sites beforehand and change a template? Although I don't want to touch the 14 hive in order to facilitate this.
In brief, you will need to use feature stapling to associate your custom master page with newly created my sites content pages (default is v4.master).
There is a useful overview of customising mysites in this blog article on MSDN.
It depends how deep you would like to modify. You can have some inline code on default.aspx which activates features on that users personal site. Then you can program and deploy a site scoped feature to the web application and it will get activated on each site when the user visits default.aspx the first time.
In that feature, you can change the override CSS options and masterpage.
The reason for doing it this way is that the stapling only applies to sites which will be created in the future from that site definition and not sites which have already been created before the feature stapling.
Using Feature Stapling is the way to go if you need to control it at the time the site is provisioned. An alternative though would be to leave the site provision and templates unmodified and instead focus on updating the masterpage settings directly. They can be set via PowerShell or a 3rd Party administration tool.
I've seen some tools offer a scheduling feature that will automatically update the setting on a scheduled basis to help enforce governance. I'm sure the PowerShell execution could also be scheduled.