Apparently, I'm offensive. So, I'll try to re-write it to keep it friendly. Logic is friendly, no?
Your expectations are unrealistic. You're wanting a bike that has 650 torque and hp, which the TR650 has. But you want it to have the fuel economy of a 250. At 260% the displacement of the 250, you should not expect the 650 to get that kind of economy. At 50-60 mpg (I'm seeing 55 mpg and I ride pretty aggressively).
The load that you anticipate hauling regularly, over 120lbs, would need to be well thought out how it was loaded to make for your safety. 60 lbs shifting mid turn will not end well. The extra weight is going to both hurt your fuel economy and the safety factor you're wanting in a larger bike. So, you might want to start with re-thinking the amount of load you want to carry.
That rack that broke was on a bike that was ridden more aggressively and over more rugged terrain than most TRs will ever been ridden in their life time. Refer to his ride report here:
http://advrider.com/forums/showthread.php?t=872817 and his reports of a long commute over rough terrain daily in various threads on here. It shouldn't be expected for a stock rack to handle extreme conditions indefinitely. For the price, it should be assumed that it is built for the majority of the target buyers rather than the extremes. That's what aftermarket is for, they just need to catch up. The bike has not been in market too terribly long.
One other thing I want to point out, is that a motorcycle for fuel economy is really just an excuse to give the wife. This maintenance costs behind a motorcycle are significantly higher than a car. Even at 5000 miles a year, you will be looking at 1 set of tires per year. Probably 2 sets of brake pads, oil, filters, chain, sprockets, bearings, grips, etc, etc. The costs of the consumables will add up beyond the price of the fuel savings very quickly. Throw in the higher insurance costs, and you really can't say that you're riding it for fuel savings. So, try not to get hung up on that part. It is a reasonable bike, that should be very dependable and last a lot of miles. You might want to give that more weight than the fuel economy numbers alone if you want to think reasonable.
How was it you came to the conclusion on the KLX250? It fits the fuel economy, but it for sure wasn't intended for that kind of weight on the tail either.