so what do you want to do with the bike, as hardly any of them will be a do all? You'll have to define your priorities, which is why most riders have 2 at least and usually 3 around.
The ninja 250 would be a good overall bike, but not for the trails or sand. A used BMW Dakar 600 would be a pretty much go anywhere, but it's tall but it gets good gas mileage, it's one of the toughest bikes out there. Sport bikes are cool looking but two things against them. One is that hardly any rider is good enough to use them for their performance level, and the ride position sucks. The Ninja 250 has a more upright. The Suzuki Vstrom 650 is also a very good one, and the new Honda 700NCX is a pretty much do everything, and I hear the mpg's are awesome. But it's chain final drive, so a shaft drive Honda NT700V is an excellent buy. Why they spent the money on developing this one, when they had the NTV and could have modded that one for taller off road tires, or put the dual clutch transmission in that one and would have opened a huge market is beyond me.
Finally you have your scooters. They are not to be derided as they have so much to offer. That's why I switched to the Suzuki Burgman 650 for my commuter bike. enormous cargo capacity, which you'll never get on a traditional bike, automatic transmission for ease of riding, especially in heavy traffic, virtually no maintenance, mine gets 54 mpg, and even better when I choose to use the optional manual electric thumbshift, which gives me an overdrive. I have had that bike up to 105 and there's still more, and it's stable as a rock. Low center of gravity because the engine is down low, and overall weighs 638 pounds. Very comfortable riding positions because you have alot of room to put your legs forward and back. I tuck mine back as this gives me the best position, but a couple of buddies have them and they ride feet forward. But it's more like the station wagon of bikes, and some people have ego issues so won't consider them. Too bad really, for what these can do and what you get for the money.
But bottom line is you need to decide what's really important, and then narrow the choices. For me chain drives are out, I'll take a belt or a shaft drive anyday. Shaft preferably for the long run. Chains just are more of a fussier thing. I like the option of the automatic and having the manual shift when I want it. More bikes are coming out with this, like the Honda VFR 1200, awesome, and basically a scooter on mega steroids. The world racers love that bike in general because it can shift faster than a human can and keeps it in the powerband ALL the time. But it's very pricey do to that.
as far as engines go, the 250's are singles, which are fine, and around 500 cc's they switch to twins. on bikes bigger isn't necessarily better as you well know, the smaller ones have plenty of power and are more fun to ride, but not on a long interstate trip. But I would hate to take the RoadKing on my runs to the grocery store. I can carry like 4 bags of groceries in my Burg. The RoadKing maybe a loaf of bread.
A 650 is a very nice all around compromise for power yet economy, the 400's are good too and there's nothing lacking there.
Hope this helps Sk8r