Some benefits of a filter holder system:
- one holder for all lenses;
- the transition area for GND's can be freely positioned;
- stacking filters is less likely to cause vignetting;
- a complete filter set weighs less as you add more filters.
I don't agree that Cokin is crap; it's an entry level option with a price point to match. Comparing a $75 Cokin polarizer to a $150 Hoya Pro is of course not going to favor the Cokin; you get what you pay for. If you want better quality, step up to Hitech, Lee or even Singh Ray. Expect to pay progressively more though.
If you do not expect to stack filters extensively, and only ever expect to use a polarizer and perhaps an ND filter, then the screw-in option is more viable. Step-up rings still allow you to use one filter for several lenses with different sized diameters.