Scott - from what little I know of your riding tastes, I think you will prefer a bigger bike simply for the expedition capabilities. A 650 with a large tank is the only bike that makes sense for LD (long distance) adventuring. They aren't that difficult to pick up when you drop it, they can hold a lot of gear, and they work well on the open road. Just like the venerable 22R motor trying to push an overbuilt 4runner, the midsize on/offs simply cannot handle the weight of LD trips.
I've had (and sold) a Yamaha XT650 and Suzuki DR650. Today I would choose the Kawi or Honda 650. The KLRs enjoy massive aftermarket support and a cult following, both brands offer bulletproof reliability. You can sleep in a broken truck for a few days; a broken bike is a whole different level of vulnerability.
I lust after BMWs and LR Defenders, but at the end of the day the cost of ownership and limited repair facilities in North America conspire to move them towards the bottom of my 'reasonable decision' tree.
You can find plenty of solid used bikes for a season of riding, and often can sell with little to no $$ loss. That lets you try one for a while, and if you love it, maybe it's worth buying a new(er) model. The 650s hold their own on the open road, anything smaller gets blown around too much for my tastes, for all-day riding at 65+ mph. The displacement of the motor contributes little to overall weight, and the HP gains are worth it. Wet weight is always higher, but we need fuel to go deep.
Tires often suck - you'll mire in tire decisions just as bad as we do for trucks.
I've migrated to LD sport touring bikes, riding a Kawi Concours 1000 last year and now a Honda ST1100, both bikes have 7 gallon fuel tanks and swallow ground amazingly fast. It took a while to get used to the weight (these are fat bastards at 700lbs) but they feel almost nimble at speed. A bigger bike is much more comfortable (relative term here) for 500+ mile days.
As you've realized, the right bike for Baja and a trip to Alaska isn't really the same bike... but working backwards, the perfect baja bike would be miserable to Alaska, while the perfect Alaska bike would be pretty fun in baja.
I'm going to leap to the conclusion you own (or have seen) the Long Way Round DVD?
m.