Are you considering only used bikes, or possibly new? The KTM and Husqvarna 350 dual sports (same bike really) are like ten grand new, and even used will run you several thousand.
I have been advising everyone I talk to about this stuff to stay away from the Honda CRF 250L because they have a poorly designed cam chain tensioner that often fails. Honda, having known about the problem since 2013, hasn't fixed it or issued a recall. I love Honda for the most part, but that kind of crap really irks me. If not for that, I really like the CRF, even though it is on a somewhat lower level in terms of performance. On a related note, I've written about this cam chain tensioner so many times in similar threads to this, that I'd be willing to BET that Honda has lost a few thousand dollars because of me lol! EDIT: This thread now shows up on the first page of results from a Google search for "fuel injected dual sports". Get on the ball with this thing, Honda!
*Yamaha WR250R: I would say this is the best sub-400cc FI dual sport available right now. Considerably more power and much better suspension than the in-class competitors (Japanese 250-ish bikes). Reliable and durable, low maintenance motor (which is why I'd pick one over a KTM 350) . Not KTM-light, but reasonably light compared to its Japanese competitors, and it carries its weight better than some of the others (better mass centralization).
*Yamaha XT250: Fuel injected since 2013. Air cooled 5 speed with power and torque somewhere between the TW and WR250R . A little over $5,000 new. Soft, budget suspension, but it's probably not too bad if you're like 150 pounds or less. A little ligher than the WR/slightly heavier than the TW. Much lower seat height than any of the other FI dual sports. From the research I've done, it should be fairly reliable and reasonably durable. I'm glad that someone offers a low seat, fuel injected dual sport option for shorter people. (EDIT [10/23/2015]: - I bought one of these ;D Here is my review of this model: https://tw200forum.com/forum/other-bi...50-review.html )
*Husqvarna TE310: No longer available new. I know a guy who bought one recently and was having major issues with the fueling, for what that's worth. Personally I'd stay away from this one.
*KTM/Husqvarna 350: Hands down best FI dual sport money can buy from any manufacturer, from a PERFORMANCE perspective (meaning off road capability but also SPEED, as in "Ready to Race"...). Much lighter than pretty much any other dual sport, with much higher spec suspension and other components, and much more power. Don't buy one unless you enjoy working on your bike a lot. The WR250R should last at least 10 or 15 thousand miles longer and require much less maintenance during that time.
*KLX 250S is fuel injected in European markets. If you wait around a little, there is a slim chance they'll bring that to the U.S. for the 2016 model. Sadly, I still would not personally recommend this because they are also known for crappy cam chain tensioners that go bad and fail. Performance wise, it's pretty nice, but not quite on par with the Yamaha in that department.
*Beta RS dual sports: they have offered several different motor sizes over the past few years, from 350 to 520 IIRC. Currently 430 and 500. Right now they are carbureted... They just recently introduced their first FI system in their 350 off road-only bike. Like with the KLX, there is a slight chance they'll put their FI on their dual sports if you wait a bit for the 2016 models. These dual sports are also very light and very high performing, absolutely top notch dual sports. Personally I'd have one over the KTM's any day.
*AJP PR5R: AJP motors has been around for quite a few years, and in the U.S. market for the past few. Right now their U.S. offerings are not street legal. I communicated with an AJP rep a few months ago and he informed me that it was likely they would be offering their PR5 as a 50 state legal model for 2016. Another reason you might consider waiting a few months, if you are considering purchasing new. This would be my number one choice for a kick ass trail/enduro bike from a performance perspective. It's very light, has VERY good mass centralization, excellent suspension, fuel injection, and similar power and torque to the WR250R. I'm not entirely sure about the reliability and ease of maintenance on these machines, but from what I've seen of them I think it should be at least decent. Probably less high maintenance and more durable than the KTM's. The dirt bike version is about $6,500. I'm guessing the dual sport version will be a few hundred more than that when it comes out.
*Honda Grom Scrambler (concept): This is another bike in that "might be available in the near future" category. The regular Honda Grom has been available for long enough now to prove itself as a legitimate mini bike. The Honda Grom Scrambler is a 125cc mini-dual sport/scrambler concept...that would make a fantastic around-town, first bike/fun bike type of "dual sport". Great fuel economy, an amazingly low entry price (for the currently available, standard Grom), a very low seat height, superb ease of use, and awesome aesthetics would make this a perfect choice for anyone on a small budget who doesn't need to go on the highway. http://www.motorcycle-usa.com/wp-con...oncept_Two.jpg .
*Then there's this... http://www.cscmotorcycles.com/product-p/zrx3-b.htm . I've done a fair bit of research into these as well. From what I can tell, it's probably okay in terms of reliability. I'm still somewhat skeptical, but it should be noted that the same basic motor powers that AJP. I think it would work out alright. This particular model is very heavy for a 250 dual sport, and pretty street-oriented. And no, that motor does NOT produce 30 foot pounds of torque...shame on them for having a damn typo on their web site, especially on something so important as engine performance. That REALLY doesn't look good IMO. EDIT: I visited the page on 10/02/2015; as of this date, the page shows the correct value for the engine's torque output.
*BMW G450X: Sadly BMW discontinued this bike. It would have required significant changes to be viable IMO. Not really a good bike, but since you asked...it is technically an option.
Can't really think of anything else off the top of my head, certainly nothing major that isn't from some tiny knock off company or whatever. I really wish we had more options. I hope Honda will give us a 300+ FI dual sport (with a non-POS tensioner!), and I'd really like to see an FI, six speed DRZ (maybe 450). Also a WR450R would be nice...