What kind of money are you actually working with? Kinda hard to give helpful advice without knowing more about your budget. Had a garage full of all kinds of different dirtbikes and dualsport bikes. Little 250's for riding trails and XR650R's and L's for longer trips and everything in between. Got rid of all of them when I started building this motorhome
. Wanted one bike I could take with me that would do it all. My XR650R was pretty well set-up and I had a street wheelset for it (19/18). Put many trouble-free miles on that thing, but my younger brother sold all his Hondas and switched over to a 450EXC. Never really thought a KTM could replace an XR, but I watched him put over 350hrs of absolutely brutal riding in all kinds of conditions on that machine. Never a hiccup. Absolutely no maintenance required beyond oil changes. That finally convinced me.
So I bought a 2010 450XCW, plated it, and picked up a set of a SM wheels. Ended up replacing the SM wheels with a set of 19/17 Woodys wheels, which I've found to be a lot more versatile. But I've put over 9,500 miles/250hrs on it so far (mostly high-speed DS and on-road) and Rob's raced Vegas to Reno and a few enduros on it. Just pulled the topend to replace the rings and found the Wossner piston had developed a weird crack, but from what I can gather it seems like a fluke thing. No other damage (cylinder still looks brand new), $150 to fix, and that's the only trouble I've had with it. Oh, had to adjust one valve, once. With close to 10,000 miles on it, there's still no play whatsoever in the rod, and no reason to think it won't go at least another 10,000 before I might need to split cases and replace the crank and rod. The maintenance intervals can be very misleading if you're not... racing.
People say they don't make'em like they used to anymore, but I think that might be a good thing. This bike is SO much awesome-er-er than the old dualsports. And they're not particularly expensive to own if you take care of them and are capable of doing your own work. No, it's not a streetbike, but there's no real reason why it can't be ridden like one. Way more performance than than a WR250, but that would be my second choice, and there are lots of good deals out there (08-11 bikes with low hours in good condition for $4500-ish?).
To me, the real issues are, 1) intended use, 2) money, 3) maintenance.
1) If you want an offroad-oriented dualsport, you know you're going to be giving something up. Comfort. Got a Renazco seat on mine and that's about it. Last big ride I did was from Bend, OR to the bay area. About 550 miles / 12hrs in one day. Honestly wasn't that bad. Wind blast bothers you at higher speeds? Get a fairing. Personally, I can't see needing much bigger of a bike. Ever. Ride 2-up all the time and it'll cruise along happily at 85mph all day long.
2) No advice to be given here. Nicer things tend to be more expensive, and while the KTM's are definitely higher-priced, think they're also high-value.
3) It's not a Honda Civic. If you just want something you can fill-up with gas and never think twice about, that KLR is probably the bike for you. But I haven't found the maintenance to be very expensive or difficult to stay on top of. Simple stuff, like changing the oil, etc.