The 250/300 motor barely changed from 1994 until very recently (2010 at least, but 2012 sticks in my mind).
The combustion chamber is old school - narrow squish band with way too much squish clearance and too high a compression ratio. This makes them impossible to jet cleanly, to minimise the effect of the old school porting.
I had my 94 YZ250 and 08 TM250 out at a track on the same day. While the TM had better brakes, suspension and ergos, there was no question about which bike had the better motor or handled better...
The bridge in the TM250 exhaust port is too narrow, and buckles into the bore when it's hot. This is probably compounded by having cool water from the radiators being dumped straight on top of the exhaust port. So the bridge cuts into the ring, until the un-worn part of the ring snags in the exhaust port, which destroys the ring, piston, barrel and power valve. This happens between 25 and 30 hours, pretty much like clockwork.
Having the bridge built up with weld (to make it wider) and then relieved before replating, is supposed to make a big improvement.
I'm also told the later ones have a redesigned barrel, but have no experience with these.
Add in the issues with threads pulling out of the sand-cast cases, and it's hard to get excited by a billet brake pedal...
(I should mention that I've also owned two TM125s, and loved them both to bits. I still have the 94 model I bought in 1997, and selling the 04 model is one of two or three biggest regrets).