Well, I actually have the 3G Kindle because it was the only model they had left two days before Christmas....The Kindle's 3G runs on the AT&T network and I was pretty surprised to find it had better coverage than Sprint in my area (AT&T doesn't really get advertised here...it's a Verizon world). I have 3G even though the Amazon website says there's only EDGE in my area and that's at my house where I can't even get a decent roaming signal (nevermind Sprint) for annoying reasons.
However, I tried it with the unauthorized MHS and had the same problem. I also tried after getting my laptop connected, however, this is a no go as well. The 3G connection goes off everytime a device is connected or disconnected, not just when the first device is connected.
Ubuntu had a problem connecting the MHS app as well due to a bug by Palm and getting around it meant patching and recompiling the wireless drivers in Ubuntu, something that's not going to be easy with a Kindle. The best I can tell you is to hope the upcoming improvements to the freetether app will bring a resolution to this issue, but I'm not sure. I know they're taking donations so they can keep improving the app for webOS 1.4.x and 2.0.x.
As to the relative merits of getting the 3G or Wi-Fi, well. The 3G wireless is free only for downloading books/blogs/mags from the Kindle store and for use with the web browser. If you have your phone with you, you'd probably be better using the one on your phone, even though the Kindle now has a webkit based browser (although very limited). For converting and sending personal documents over the 3G, it's $0.15/MB rounded up to the nearest megabyte. So if you don't want to pay everytime say, Instapaper sends you a file, you'll be sending things to your free Kindle email address that only delivers over Wi-Fi anyway. Further, with the Kindle you have free access to AT&T wifi hotspots that others normally have to be on AT&T for or pay to use.
On the other hand, I much prefer reading Instapaper on its actual website as opposed to how it looks when you send it, because I don't like the way the Kindle navigates periodicals. You can also create a collection of bookmarks easily accessible from the Home menu here (Kindle Start Page Tool) if you think you'll be using the browser a lot - and with 3G, it could facilitate your browser use. It's an added convenience if your Pre is about to die and you need to check something on the web. Further, if you think there are things you'd rather do on a Kindle than on your phone, having the 3G would be a good option. This is also true if there are sites with items you can download directly to the your Kindle if you want to be able to download them whenever - for example, you can download free books from a few different websites at no charge and already have them on your Kindle. This can be done on wi-fi, of course, but if you live in a area where hotspots are scarce or don't care to be dependent on them, then it's easier with 3G.
Whichever you choose, get the graphite one.
While I'm here, I'll also show you the case I got for mine: Belkin Pleated Kindle Sleeve which comes in four different colors (I got the purple one). I like it because it doesn't add a lot of bulk to the Kindle, it's lightweight, and it's easy to get the Kindle out of it without making a lot of noise (there was one case I really like, but it used VELCRO...pitiful). It also has a pouch in the front where you can put the Kindle usb cord and charger, so I don't have to remember where I put it at (bonus benefit: the Kindle's usb cord works with the Pre, too). Someone in the reviews for it mentioned this one as well: M-Edge Latitude Kindle Jacket for those who would prefer not to take their Kindle out of the case and because it has a pocket for a light if you have one. But I like the way the Kindle feels in my hand, so I got the first one. Great if you just want a little padding to cover it while you're not using it in your house or to slip in your bag.