I dunno what other people's 401k plans look like, but I've got about as much flexibility to invest as I do with my Roth IRA, and pay less in fees. A lot of that's because I knew more about finance when I set up the 401k, so I was already on the index-fund bandwagon and didn't pick it because, say, my dad had an account at the same firm.
Fund selection and account type are mostly orthogonal. The reason to decide between a 401k, IRA, Roth IRA, or individual account are tax and withdrawal considerations, not investment decisions. Then you make investment decisions within the account based on where you want your money to go.