While I tend to agree with you about the 'dirt' capabilities of the KLR -- too big / too heavy -- I do, tho, think they make passable back-road touring bikes.I think the OP wasn't planning on using a KLR for a dirt-bike? I think he was looking for more comfort -- and, I think I can agree with that.
As for reliability: KLR's have had 'issues' -- plenty of them (besides the infamous 'doohickey'). They are kind'a "built to a price"...
My direct experience with them has been entirely internet-based other than a friend with a
KLR-600, which was not entirely new.
As for back roads, they're hard to beat for riding any sort of distance on iffy roads. There are bikes better (KTM?) but nothing at the dollar.
After 8 months direct experience with an '09 there are precisely these "issues" most deal with. Some changes depend on how much dirty riding you want to do. Prices are memory guesstimates. Many parts can be found used. The KLR gets bashed a lot by some because it isn't a KTM or BMW. It doesn't try to be. Some care, some don't. Then again, rear drives and difficult to find parts and dealers are not a KLR issue.
1) Bash plate and Nerf bars are needed to protect the oil pan, radiator and plastics. Two major manufacturers available. About $250-300 depending on style, etc. I'd recommend a $12 low profile magnetic oil drain bolt at the same time. The stock bash plate is heavy plastic and good enough for well-maintained gravel roads, but not much else.
2) The Doohickey is stronger on the '09, but I swapped mine out at 69 miles to avoid catastrophic engine failure. Cheap insurance at Eagle Mike Manufacturing -- <$50, but cracking the cases for installation requires special tools and either guts or some mechanical skills -- or a good mechanic.
3) If you are going to beat the bike up or run exceptionally heavy loads, the Frame bolts need to be upgraded. Again Eagle Mike is the community standard. I haven't done mine yet, but I will. Less than $50 in parts.
4) The engine can burn some oil if you regularly run at high speed (a relative term on a KLR) and high RPM. Some don't burn any oil. If they do it is @ 1 quart per 1000 miles (in my experience anyway when I ran high revs). A permanent fix for oil burning (if you are unlucky or run at high revs) is to bore out the cylinder with a Schnitz racing kit of 685 or 705 CC's. I think the kit runs @ $350-450 depending on size.
5) Stock hand guards are great for wind breaking duty, but useless in the event of hitting a tree limb or something. If you are going to do that, buy some ascerbis or barkbuster aluminum guards (the community favorites though others like Moose are appreciated by many). Less than $100
6) The rear master cylinder is vulnerable. A $45 part protects that. Some go ahead and replace the stock mounting bracket at the same time for a few ($40) more dollars.
7) The cooling system was improved in '08 and carried over to the '09 -- the problem is the bike runs cold and for some, with fluctuating temperatures. A fix is available called the Thermo-bob at @ $150.
8) Some swap out gearing to obtain lower highway RPM or shorter gearing for off road work -- totally up to you.
9) A Clymer manual runs @ 30 bucks, a Kawi shop manual double that.
10) It's a thumper. Locktite is your friend. All thumpers shake -- get over the mechanical sounds (I like them) or get another bike.
The '09 fixed many of the problems with earlier models. The brakes were upgraded; the shifter and brake pedal were improved, though not enough for very heavy duty. The plastic added a couple pounds but much better air management. Like the FJR it feels lighter when moving. Like the FJR it could benefit from suspension upgrades, but the suspension was upgraded by Kawasaki from earlier models (the A model specifically). The '08 was the first year of a major upgrade, and recalls occurred on the harness (rubbing in places) and the exhaust bolts falling out (fixed at dealer prep). The rear luggage rack was increased in size, turn signals were improved (though some early ones dropped off but easily put back on). The battery is a wet cell design and some in hot climes swap to a mat cell design. I have 1600 miles and just checked -- no distilled water needed. The charging system is not overwhelming, but will run an accessory or two.
I think that covers it for commonly understood deficiencies. I may have forgotten something, but I'm sure it will be pointed out. You can do the math. There is a KLR everywhere, people are around to help and if you can do your own work, the bike is VERY cheap. I don't love the KLR in the way I love the FJR, but I am very happy with it -- with that, I think I can give a fair and unbiased view of the pluses and minuses. If you are going to fly over berms or track through woods in narrow spaces, get another bike. But if there is a half-decent trail, the properly set up KLR should get you there. Many people have gone around the world on KLR's (and other bikes), so it can't be too bad.
A huge resource is KLR650.NET and ADVrider.NET -- I find the other sites OK but not as good. More bashing of the KLR on ADVrider, but good info for rides, parts, etc.
YMMV