I'm primarily an iOS user, but I have used Android quite a lot. But, for me, Stock android has some advantages.
- Security. While Android doesn't have that great a record for security, Google have a very good team looking for and eliminating vulnerabilities in the android components they provide. You don't know that your phone company (or whoever provided the interface your android install uses) does. Google are far from perfect, and have a disturbing habit of spying on their users, but they will have the ability to do that whatever install of android you have.
- Extra software (such as different interfaces, dialers etc) uses extra resources from the phone. This can mean limited storage for user data/apps, and also slow the phone down. This isn't an issue if you don't use apps, but can be if you do.
- You don't get a load of crap software installed because the manufacturer of the phone is being paid to do so by another supplier
Thankfully, Apple, as one of the restrictions of using iOS, don't allow the carrier (or anyone else for that matter) to replace parts of iOS (such as the dialer). In later iOS versions, they've softened that stance somewhat and do allow alternatives to the built in functions of the phone (such as alternate diallers and messaging apps), but they always require that the original function is left available if the user wants it. I still shudder when I think of the awful pink, white and grey dialler software T Mobile insisted I used on my HTC tytn instead of the standard Windows Mobile dialler.