I think we just have to put aside our greed as homebrewers and accept that we're going to have to leave some beer behind when you dry hop with pellets. They will either fall to the bottom or float on top, so just stop the siphoning early enough.
I generally prefer pellets because you can clearly see them get soaked in beer and you know they're distributing their goodness. I've dry hopped with whole cones and sometimes it takes a week just for the last few to soak into the beer. However, one thing I like about dry hopping with cones is that I frequently reuse the hops as bittering hops in my next batches... yeah, sounds crazy but remember that greed thing I mentioned above? Well that also means saving money on ingredients whenever possible. I just rack the beer off the dry hops (and usually bottle), rinse the hops, and then toss them into the brew kettle. I anticipate a little less utilization, but I still do the calculations as if they were fresh hops and then settle for less bitterness in the final beer.
