The only "must do" upgrades I found were to higher end brakes (The Oryx brakes are...squealy. there's not enough metal in 'em to keep them stable) and the seatpost (which was...bad. Very bad. Didn't hold the seat, which seems to be a bit of a "must do" for a seat post).
I love my LHT, but I have the same complaints about the front brake and seatpost. I bought the bike in mid-March and have 1,000+ miles on it.
With the brake, I've read here that it is Surly's choice of a cable hanger setup that causes the squeal. The Kalloy seatpost was simply a poor design and easy enough to switch out.
I needed a complete bike in a hurry after my commuter got hit by an SUV. I've been very happy with my choice.
As for all the people on BF who tell you to test ride several models before making your choice, that's easier said than done. Shops just don't keep a lot of sizes in stock, and it would be useless to compare a 62cm LHT to a 58cm 520 or a 60cm Aurora. And the shops won't order a bike in your size without a hefty deposit or full purchase price down.
So I chose the LHT because of its great reputation for loaded touring (I haul a lot on my daily 22-mile RT) and because it was available in my size right away.
The bar-end shifters are great. I'd never used them, but have extensive experience with brifters and downtube shifting. I find the bar ends easy to use and rock solid.
When it comes to higher-end components on road bikes, IMO, what you get for your money is mainly a few grams lower weight and the prestige of the brand, but not a lot in functionality or durability. The components on the complete LHT are of the heavy-duty variety, which makes sense. To go with high-end road components on this bike would be like putting racing tack on a mule.