I'm always a little surprised when someone who hasn't ridden one mile on a bike declares that they're going to have to spend $4K on accessories like seats, windshields, footpegs, grips, etc. to make it acceptable. These are all things that you'll never find out if you need to replace by reading the internet. Instead, you've got to put in some 500-miles days and see how it all works for you.
I'd recommend you get the FJR and leave all the extra money in the bank earning interest. Unless you really want the BMW, it is hard to justify the extra money. Ride it for awhile and then one by one, fix the things that need fixing, asking for advice as you go. It may be a lot of things, it may be nothing.
This is one of my huge pet peeves - way too much internet riding rather than real riding.
- Mark
Well, then let's get away from Internet riding, and into real riding.
I own both a 2005 FJR (full disclosure - put up for sale today) and a 2006 BMW K1200GT. I have toured on both, putting 12,000 miles in under 6 weeks on the Bimmer last summer, touring across 23 states and two Canadian provinces; and 8000 miles in two summer tours over about 3.5 weeks on the FJR in the previous summer.
I feel that after owning, rather than test driving or reading about, both, I'm in a pretty good position to respond to the original question posed; at least with an opinion as to how I see it.
First, the Bimmer offers some advantages over the FJR. Even cooler than the 06 and 07, both of which I have ridden in summer. Cruise control factory installed versus aftermarket (YMMV), which performs flawlessly. This is a big deal to me. Slightly (IMHO) superior brakes. Suspension adjustment (9 settings) with the ability to change the 3 gross settings on the fly (a feature that those who have never had it indicate is unnecessary; much like many of those who shrug off a need for an electric windshield until they've owned one and are willing to admit it). BMW: Superior fit, equal finish. Bags that don't require a key to open. Superior lean angle, stock-to-stock. Both now have integrated (on my 2005, the control sits above the bars like an afterthought) heated grips, bmw offers factory installed multi-level control heated seats. Trip computer with more functions.
On the FJR side of the advantages tally book, you have the ability to add highway pegs (the bmw has no place to bolt these on), a metal tank for those who like magnetic tank bags/map holders. The stock seat on the FJR is so far superior to the BMW's its laughable (altho I still run a Sargeant seat on the FJR).
I've modified both with aftermarket shields, peg lowering kits, and risers, so for me the comfort level/position is equivalent, although for some reason the FJR feels slightly like a better 'fit' after 300-400 miles; but I couldn't tell you exactly why.
Now for the hard part; the price and maintenance cost difference - i.e. the elusive 'value for the buck' calculation.
My honest assessment after having ridden and owned both is as follows. The BMW K1200GT is a superior bike to the FJR. This would be my opinion even compared to the 07 FJR, which is a huge advance over the 05 in heat (I did the Cromeit heat fix which solved the bulk of the problem), but which seemed to me (IMHO) to drive/ride very similarly to my 05 in all other aspects. BUT, does the degree in difference in superiority justify the difference in price - I personally don't think so. If you have to justify the additional amount of price and ongoing cost with the difference in the bikes, you can't. The FJR is the clear choice. BUT, IF the price and maintenance cost is of literally no consequence, and all you want is the best sport tourer available, than the GT is a better pick than the FJR (which constitute #1 and #2 in the list of good choices).
Everything here is my opinion only, but is at least based on weeks in both saddles.