I bought out of a desire to do some touring, what prompted me was our very own Ride Tales section. I had two superbikes and that meant duplication, either one could do the long haul. So I revamped everything, traded my 916 for an 07 1100S and sold my 999S and bought an upgraded 999R. Best motorcycle decisions I have ever made.
I immediately dove into fixing some of the minor glitches the Multi may or may not have, depending on the owner. The two I discovered was inadequate wind protection in particular against wind buffeting and a means to smooth out the power and make the bike less jerky at slow speeds. I found the solution to the wind problem by doing research on various windscreens and settling on buying the MRA Vario windscreen with adjustable spoiler. I thought highly enough of the MRA that I worked with Motowheels on putting together a group buy over on a Multistrada specific website. By last count the thread is around 160 pages and the initial group buy number of screens (20) might be sold out. However, Motowheels still has them in stock. I found immediate relief with the screen against wind buffeting, the main culprit. Now I can cruise down the highway without getting beaten up. The wind that does hit me is clean and just at the top of my shoulders. I found by adjusting the multiple settings on the screen there is an optimum position there for just about anyone's shape. Its an extremely well made and hi tech looking screen. Its closest competitor in concept only is the Laminar Lip, the only problem is the fact the Laminar Lip is ugly by all accounts, isn't adjustable and only comes in clear.
The second issue for me is the aforementioned jerkiness one may experience with their Multi power. This issue can be resolved simply and reasonably. Whether you put on an aftermarket exhaust or not, install a FatDuc manipulator which in essence fools the ECU into a less lean mixture. Multis come from the factory a little on the lean side, even more so once an aftermarket exhaust is put on. However, I have found out of all the exhausts made the Zard product seems to work best with the stock ECU. It wouldn't matter anyway because I would install a FatDuc regardless. You can get by with a de-cat eliminator pipe which removes the ugly "utter" cat underneath the bike without any add ons like an ECU or PC, but if you were to add one more element to your aftermarket modification you have to add something to resolve the lean fuel mixture issue. Based on all the stuff I have read the FatDuc is the business.
You can add to the benefits of the FatDuc by also installing iridium plugs, they have the ability to smooth out the low end power and by having both all of the loose ends are covered. I just installed the iridiums last week and have yet to test ride the bike because its been well over a 100 here since, but I did notice a smoother response as I throttled up off idle. No imagination there, it was real so I expect some nice results on the test ride. I haven't gotten around to installing the FatDuc just yet, but I will. Another board member here (Olaverez) just emailed me in regards to his new Multi. He just traded across his black Multi for a red one. What he found amazing was the difference in power delivery between the two bikes, the new red bike being so much smoother than his 08 Multi. He indicated the new bike is equipped with both the FatDuc and the iridium plugs. The improvements Olaverez described are exactly the improvements others have detailed after the FatDuc was installed. It is unknown at this time how much the iridiums contributed since they were both installed. I'll be in a position to feel the difference once I have had a chance to test my bike and later on test it with both products installed. He also said his bike is running much cooler than what he was accustomed too. The only downside to the improvements is a lost of some fuel economy, this hasn't deterred anyone that I know because the benefits far outweigh that.
The seating issue is a personal one. Some people have no problem with the stock seat, a vast improvement over the earlier Multis. I went on my longest ride yet last week, about 6 to 6.5 hours in the saddle with breaks. My butt was sore going home, thats for sure so in my case I would likely upgrade to improve that situation. The latest I read about that subject indicates the DP gel seat isn't that great, there are others we are familiar with like the Sargent or Corbin also the Airhawk has some good reviews.
Lastly, I would have the suspension dialed in by a guru and eventually set the bike up to handle heated gear (great stuff). The bike is likely one of the best all around motorcycles available. I like the fact if you want to dice it up in the twisties, it has superbike heritage with the trellis frame and full Ohlins suspension (S, however all 09s are S models now). Of course you then have the comfort and up right seating for the long haul as well.
The 2010 model will see a drastic change with the introduction of the water cooled 1098 motor. Mixed reviews at this stage and personally I have no desire to trade mine in. One big reason is maintenance and the other is I'm very happy with the power the 2V motor produces. If you ever do your own maintenance the 2v is traditionally the easiest of the bunch to do and the motor has always had a very good reputation for reliability. One glitch from 03 to 06 was the weak valve guide problem, a hit and miss issue. Likely had to do with sub letting again, like the old rocker problems of the earlier superbikes.
Good luck with the bike, I certainly like mine, it is just so much easier to ride compared to a Superbike.