I recently purchased a 2004 TTR 125 and have been riding trails. The bike has mostly sat in a garage during the last 4 years and now that it is being ridden regularly it tends to stahl out after being started instead of idling and when riding a trail or road and slowing down or coming to a stop it dies. Normally it will start again after 2 or 3 kicks, but even though it is warmed up it will die again when coming to a stop.
Two good points here. Clean the pilot jet. Nine times out of ten if a bike won't idle it has a clogged pilot jet. Remove the jet and make sure you can see through the center hole.
Also, like dirt bike dave said, check the valves. If the bike runs worse when it warms up it is usually caused by tight valves. The hotter the engine gets the tighter the valves get.
I had the same problem on a 03 ttr 125... I cleaned the carb and it works great now... Let me guess it will idle with the choke on but as soon as the choke goes off it dies. Just clean the carb really good and you'll be back in business.