I have always just dumped my pellet hops directly into my boil kettle with great results. Wort clarity has never really been an issue for me as I constantly recirculate the wort with a RIMS system during the mash. I also usually do a 6 week primary fermentation, and 12 week conditioning to alleviate a lot of the cloudiness. Most of the wort clarity issues come from chill haze anyway which are proteins that can be dealt with by doing proper mash schedules, sparges, and cold crashing the beer. I usually use a plate filter if the finished beer needs further clarity.
As for the mess, I have a B3 sculpture which has a 1" ball valve on the boil kettle. I have never had clogging issues while pumping wort into the fermenters.
I know a lot of people who use homegrown fresh hops or whole hops, and like the filter bed the hops provide in the bottom of the kettle. I also know a lot of brewers who use muslin bags with much success as well. I think it really comes down to personal preference.
Lukehenslick@Facebook.com. on tap: easy virtue blonde, fruity monk belgian wit. primary: American pale ale, American stout, blow your top steam, and heffewitzen