In a word: reliable
I realize this thread is about the 2012 model, but I wanted to provide my experience with a 2009 model to lend some perspective.
I've owned my 2009 690 Enduro for less than two years (purchased in April 2011 with less than 1,000 miles on it)... in which time I've put more than 80,000 miles (yes, you read that correctly) on the bike. In that time, I've replaced a few things: intake rocker (at 31K), stator (at 47K), water pump seals (also at 47K) and rear wheel bearings (at 56K - the replacement was precautionary, had water/mud get into the sprocket carrier after getting a rock lodged in the spacer). KTM updated the rockers with a new bearing design in 2010, so when mine broke, I installed the updated version on both the intake and exhaust sides (and no issues since). I certainly recommend a re-valve of both the front and rear suspension... the front is much too soft and the rear is too sluggish from the factory.
I do oil changes every ~2,000 miles (my rule of thumb is 1,000 miles per liter of capacity, regardless of factory recommendations) and I've done a few mods to the bike (mostly convenience - grip heaters, RAM Mount for nav, turn signals in handguards, etc), but I ride an average of 1,000 miles per week... which means I need a good historical record of how long tires, brakes, bearings, etc. last. I have kept an accurate record of every oil change, suspension service, etc, so I can determine the service life of most items on the bike. Most things haven't worn out... I go through tires and oil/filters, but that's about it.
I have mapped, re-mapped and tried various mods with the airbox and throttle body, both with the XC1 (KTM Diagnostic Tool) and with TuneECU. I have little in the way of recommendations here, but I can say what's worked for me is the EVO map with a few tweaks (I use an open airbox cover and Wings exhaust). If you want smooth throttle response, with little or no "chug" you'll have to learn to do a proper calibration of the TPS and adjust your cables accordingly. Do this adjustment at least four or five times, following the instructions (posted on this forum and others) religiously. DO NOT trust a dealer to do this correctly (unless the tech owns a 690), learn to do this procedure yourself (buy a service manual if necessary). There is no substitute for doing this procedure correctly and a seemingly insignificant amount of voltage disagreement between the throttle-side TPS and the servo-side TPS can result in a "hunting" condition.
I ride every day, in every weather condition and on every type of terrain (single track, interstate, Deal's Gap, etc), so my assessment has been thorough over the past twenty or so months. I would ride this bike anywhere, in any weather and I often do. As I approach the 100K mile mark, I will have to replace my clutch (discs) and put on my third set of brake pads, but I fully expect to go another 100K miles on this bike.
I would have to say that this has been the most reliable bike I've ever owned (and I've owned Hondas, Yamahas, Kawasakis, Suzukis and other KTMs)... YMMV.
If you're considering a 690, feel free to PM with any questions.