Since I just pulled a complete 180 and went from an FJ-09 to a WR250X I thought I'd give my two cents.
FJ-09: Great all around bike overall. Super comfortable for long distances and commuting, with great wind protection, very strong heated grips, ABS/TC standard, 12V outlet, big tank and decent MPG for long distances, etc. In spite of all that comfort, though, it pulled hard anywhere in the rev range and somehow in the twisties it hid its weight very well and was a lot of fun to play with no matter what type of road it was on.
The only downsides were the weight was pretty apparent at low speeds and while splitting it made you aware that it is a big bike. Also, working on it was never very easy.
I think overall, for an only bike it is one of the ideal ones. I was able to commute 450 miles a week M-F and still go on 100+ mile rides on the weekends, something I wasn't able to do on a sport bike.
WR250X: Definitely swings way high on the fun vs comfort scale. I've always liked slower vehicles I could safely wind out on the street and that really is part of the allure of this bike. Everything about it also so forgiving, which makes it easier (and IMO more fun) to ride. I also really like the fact that I can ride it pretty much anywhere (up and down stairs, curbs, etc, and it's narrow enough to fit almost anywhere).
Also, MPGs are better, parts are cheaper, insurance is dirt cheap and the bike is so incredibly simple to work on. Everything is pretty intuitive even without a manual. Since it's essentially a dirt bike I don't care as much about dropping it or letting others ride it, either.
On the downside, there is pretty much no comfort to speak of. Reliability is also an unknown for the mileage I'm planning on putting on it but with the money I save on insurance and parts I can probably afford a few engine rebuilds along the way.
Granted, I've just gotten the bike, so I'll have to see if I can put up with the lack of comfort. I really think the FJ-09 + WR250X would have been the perfect garage for me but unfortunately I can't afford to keep two bikes at once.