The Pilot, in stock form, works very well.
You've just managed to stumble across a crew of people that is always looking to make it better.
The front shocks are the weak link on the Pilot in the suspension dept. As has been said, Works shocks appear to be the general "bolt on" answer. I have no experience with Works on anything other than my XR 50's, so I can't say yea or nay for the Pilot, but I've been quite satisifed with them on my 50s.
The rear end's fine for general stuff. Many people have been messing with the oil in the shocks - change it out for some other weight - and then recharging the nitrogen in the shocks. Odyknuck can give you a bit more info, as he just did it this week.
With some very minor mods (shocks, as mentioned above) the stock suspension can be made very supple and work quite well.
With some semi major mods, you can get both ends working exceptionally well.
Up front a change to +2" a-arms (meaning the a-arms are 2" longer than stock) and aftermarket shocks is great. I think it's probably one of the most common front end mods.
There are a few people/mfg's that are making extended a-arms, just ask if you need more info. - ask the board, that is. I don't want to put one of my buddies on the spot saying "So and so's making arms" w/o him wanting to make more.
Some front end kits require the relocation of the upper shock mount. - it's an easy thing to do if you have any sort of fabrication skills.
On the rear end it's a bit different. You can do just shocks, but you won't get much more travel, if any. BUT the damping characteristics and spring rates on the shocks will more than make up the difference (this means it's a good thing)
If you rework the upper rear mounts and switch to a shock that has 8.5" of shaft travel, you can increase the rear's travel and make it work very, very well. This takes a bit more modification work, though. There are as many different ways of redoing the rear shock mounts as there are people doing them, so no way is wrong or correct. You just have to make sure that at full droop you have NO hint of bind in the inboard CVs or you'll break them right off the tranny very, very quickly.
I set mine -
http://www.yellowdogracing.com/frankenskeeter.htm - up so that the CV's just barely started to bind then pulled the suspension up by .500" so there is no bind at all. Install the new shocks on the lower mounts and they'll show you where the upper mounts need to be.
Then you can get crazy. ATV Racing makes THE long travel kit. It widens the rear end about 4" overall (I think it's 4") and the front is widened 9". You get right at 10" of travel in the rear end and about 10-11 up front. It's an expensive kit and requires a lot of modifications, welding and such. but if you're going to be running in the desert, on MX tracks, places where you run the thing near the top speed and such, it's the way to go.
Spring rates are very important too. You need to set them up for your weight, the type of riding you plan to do and such - this can get pretty deep, so I'm not gonna go into it too much now. I don't know what rates are good for stock dimension suspensions, anyhow.
One last thought. A well setup LT Pilot will pretty much walk away from most things (quads, mx bikes - depending on rider's ability and balls) in whoops.
There are single seat vehicles out there that will trounce a Pilot in certain conditions, but overall, a Pilot's got the range covered and does everything in a very friendly, user happy way.
