The klr can be the best bike ever, but shouldn't these problems be addressed by Kawasaki instead of having to spend so much to remedy?
It's the "pay me now, or pay me later" syndrome. You can buy a bike without these issues for more money, be that a KLR with the issues addressed, or a different manufacturer's bike that costs more, or you can buy a KLR and address the issues.
There's also the ignore route, too..
Also, look at what you're talking about as far as fixes. The only one I consider manditory is the Doohickey.. $50, and a little time and that's solved. If you ask, someone in your area would be happy to assist and it's a good way to meet riding friends and also learn about your bike.
As far as the rest you mentioned, none are required. The headlight works fine, and while it could be brighter for night riding, it does work.. If you want it brighter, I'd suggest going with a relay kit from Eastern Beaver http://www.easternbeaver.com/
Taillight is perfectly good, and it's just as bright as every other 1157 bulbed tailight on 80% of the bikes on the road. If you want it brighter, an aftermarket LED unit can be had for $50 from various vendors, including http://www.cyclenutz.com/
Brakes are a bit squishy but work just fine (or DOT would make them fix them) and can be made better with a set of brake lines for $75 or, if you're really itching to stop, an oversize rotor kit for $215ish.
Skid plate isn't an issue unless you're doing a lot of offroading and wish the extra protection from rocks kicked up from the front tire. $95 fixes that issue.
Suspension works fine also, depending on how much you push your bike.. If you need it, a set of Progressive front springs can be had for $80 and a bit of heavier oil will also help. The rear isn't that bad and I know many who're very happy with the way it works.. Or you can go very high quality aftermarket for $600.
Oil consumption on the Gen 1 bikes is hit or miss. My 02' uses a little oil, while my friend's 98' uses none.. Both have 20K+ miles and neither have changed how much oil they desire. With mine, I check and fill before longer day rides, and if I'm going to be gone for a few days and putting on more than 1000 miles during the trip, I take along a quart of Rotella, or stop at Walmart and buy a quart..
As I mentioned, none of these, other than the Doohickey HAVE to be done to have a fun motorcycle to ride.. What I didn't mention is that all the mods I show here, I've done to my own bike to make it more fun for me.
(I only have braided brake lines, not oversized rotors)
I put several thousands of very enjoyable miles before doing any of these mods. I could have purchased a KTM for $2-3000 more and not needed the mods, but I didn't have the money when I bought the KLR slightly used for $3000. And looking back, I think the KLR has given me a lot of smiles, and I've learned a lot while installing the mods I've done..