Being a hop grower and a homebrewer, I would say whole cone hops out perform pellet hops any day! The main (and maybe only) advantages that pellets provide is more logistics than quality. Pellets can be stored longer, take up less storage space, be slightly more consistent, and many larger breweries simply aren't setup to brew with whole cones (no false bottoms, hop backs, etc.). However there are certain qualities in whole cones that just can't be obtained from pellets, this may be due to the extreme stress the cones go through to be heated, pulverized and formed into pellets. Breweries like Sierra Nevada only use whole cones, because they just can't get the hop profile they like out of pellets. On a more practical level hop pellets can really clog up your bazooka screen or false bottom causing a "stuck" situation when transferring to your primary. Pellets also tend to team up and stick to the side of your primary and kettle thus oxidizing. If that gets in your beer it tastes awful. Also with cones you are only pulling the oils from the cones and then the cones get tossed out as opposed to pellets which will just flow through and end up in your primary so now you have all of that leaf and plant parts of the hop sitting in your beer until you bottle and keg. We only sell our hops as whole cones and have convinced many brewers to retrofit their system to take on whole cones, and they have been more than pleased!