I've had an 1150gs along the way as long as an '05 Wee, Tiger 955i current 1050 Tiger and just purchased 2011 Wee.
Many people find the Wee comparable to a GS, in my mind its not for a number of reasons.
1. I like the way the telelever front end on the GS works, lack of brake dive makes the bike more controllable.
2. The GS has flat out better brakes than the Wee, the wee brakes are adequate, not any more.
3. The GS has a much more powerful alternator. The wee is weak in this area if you have intentions of running many accessories.
4. The GS is a flat out better designed package. For example, the bags are keyed to the ignition. The heated grips are integrated to the bike.
5. Given a choice a shaft drive is a potentially nice thing. If it matters to you then you know what your choice is.
6. The tubeless spoke wheels on the GS are trick, potentially better in rough areas.
7. The GS runs easier at highway speeds than the Wee. Its not a big deal but it does.
The Wee has the advantage of being a lot less money, they are toughly made and the 650 twin is a jewel of a motor. It is also somewhat lighter.
Suzuki saved saved a bunch of money on lower end brakes and suspension components.
I'm not sure about maintenance costs. i hear people bitch about bmw costs all the time but I am of the opinion that if you took any bike to a dealer for service and had it done by the book they are all expensive. If you are doing most of it yourself then it comes down to whats easier in the garage. Most BMW maintenance isn't especially hard, valves are simple.
So having said all that why don't I have a GS? Largely because I am not especially enamored of the local BMW dealer and I do really like the local Triumph dealer. Being on my second triple I really have an appreciation of that engine design. The wee entered the picture as a low cost back country bike that I wouldn't be all upset about when it falls over. I have no intetntion of taking it on a ride lasting longer than a few days (although I know I could).
I think that you really need to analyze the most important things to you, then go out and get in a good test ride.
'10 Tiger 1050
'09 400 Burgman
'01 HD FXD