My two cents;
It is my understanding that for an engine to be efficient it needs to maintain about 180F in the water jacket area, minimum. As was posted in this thread, albeit for emissions reasons, a cold engine is dirty engine, and this is because that as we all know when a motor is cold it needs the choke to get started, just as a car engine needs a choke or cold start setting with the injection system until it warms up, IE gets heat in the motor to become efficient and burn the leaner mixture that is present without the choke or enrichment circuit. Ideally, the T stat in a motor maintains an operating range where in the motor runs efficiently, running the motor either too cold or too hot is going to make the motor too lean or too rich. Who has not been able to tell that the bike is getting hot because the throttle response is starting to get "spongy"?
Remember, there were T stats around long before emissions were a worry. As was stated, they do produce some flow restriction, and this only becomes a problem when conditions become more extreme, such as in low speed riding with very little air flow across the radiator, which is not a problem on a car as the radiator has so much built in cooling capacity but, on our bikes we are limited by size but they are as big as possible to keep the bike from over heating, and that's where the fan comes in. In a car we all know that there is a fan to pull air across the rad to assist in cooling. In the "old" days this fan was directly linked to the water pump shaft, as technology progressed there came the fan clutch which allowed the motor to spin without spinning the fan until it got hot then the fan clutch would lock up and spin the fan. This was an easy way for the manufacturers to come up with 10 or so horsepower, and it increased fuel mileage as well since you weren't always spinning the fan. On some cars nowadays there is just an electric fan that is actuated by a temp switch like our bikes.
I remember on my 86 250 KTM which of course did not have a T stat, there was a guide about how much of the radiators to tape off once the temperature decreased below 60 degrees. As the temperature decreased further in 10 degree increments you added another strip of duct tape across one side then the other to the point where if you were riding in temps in the 20's one whole radiator was taped off and the other side was half taped off. This was two fold, to maintain the correct operating temperature range, and to keep the motor from cold seizing. So, if you think about an "Enduro" type bike where the riding conditions can vary tremendously, from tight technical stuff, to very fast open riding, the air flow across the rad and the resulting cooling varies tremendously as well. Whereas a track type bike is going to be ridden hard and with one assumes greater speed. The engine will be producing a lot of heat as well. Where again, the Enduro type riding has a mix of riding really hard, and then you might be going relatively fast but not necessarily using a lot of horsepower and thus the motor isn't producing as much heat.
If it was me, and for the types of conditions that I ride in, which are greatly varying, I would leave the T stat in and add the electric fan. On my 04 the regular fan is too big to place in the normal position because the tank is too close to the rad, however, I am told that it will fit in the center and I am looking into that. I am also buying an 06 tank so that I can add a fan for sure. Sparks has come up with a good winding spec for the Kokusan stator and I will be sending mine off to him for a rewind and then convert my system so that it all runs on DC. As when the fan runs a lot it will pull the battery down. And in the future I may even add the T stat set up to my bike depending on how it all works out. If you remember, when the 05's came out, you could buy an "upgrade" kit for your 04 since so little had changed. This kit had in it, if memory serves, the newer kick start lever, as well as the T stat and the plumbing.