Pellet hops are the way to go for most homebrewers. Unless you can get access to really fresh hops from a farm, then it doesn't really matter. Personally, I haven't found it to be difficult to track down certain varities in pellet form. If my local homebrew shops don't have what I need, morebeer.com or one of the other online retailers always comes through.
Hops will stay fresher for a longer period of time in pellet form because they have less surface area exposed to oxygen then whole leaf. So a good portion of the oils are sealed within the pellet, which helps to protect them from breaking down. With hops, freshness is everything, since the wonderful oils start to breakdown after harvest, giving way to a more vegative taste.
Plus, pellet hops have better utilization, since a good portion of the oils are sealed from the oxygen. So you can use less to achieve the same amount of bitterness or aroma with pellets, then whole hops.
As for them clogging your equipment or drainage issues, these are all things that can be addressed with the proper equipment. I use a hop stopper in my Kettle, works great. I'm not really one to let my equipment dictate my ingredients.
I recommend you conduct a test, and see if you can taste the difference.
If you ask your favorite craft-brewery which they prefer, pellet or whole hop. It's been my experience that most will say pellet. The reasons they give, because the store longer and have higher utilization, so they can use less to save cost.