This might come in handy for someone eventually, so here's what I've done to my TTR-225.
Installed Big Gun Exhaust System, changed main jet from 130 to 135 or 140, drilled out brass plug to get to main needle jet screw and turn the screw out 1 and half turns. Took out the rubber air box snorkle.
The exhaust change cost me about $400 and greatly improved the low and mid power bands (to me at least). 1st gear is a real tractor of a gear now, 2nd is what I use to get moving in and also a great tractor gear (this is also the gear I start my stand still wheelie attempts in). 3rd gear is a bit more torquey now around the middle and high end and is where I do a lot of my trail riding at. Up around 5th and 6th this beast really gets moving, to fast for me, but my riding buddies say it's pretty quick. I don't know if taking out that snorkle helped much, seems to, but then again I don't know for sure. I figure more air in is good sometimes.
I've changed handlebars several times, I use the cheap-o $30 aluminum ones. I have seen the adapters that change a 7/8 inch bar to a 1 1/8 (Fat/pro-taper) type bar, but I haven't gone that route yet.
The front break and clutch levers have been changed out several times to. I don't use the Yamaha TTR-225 specific ones (I hate waiting for special ordered parts to arrive). Instead I use off the shelf XT225 levers or 93'ish YZ125 levers.
My opinion on this bike. I love it! Ya it's a heavy beast.. about 270 pounds wet or so maybe a little under powered. However this being my first bike and me weighting in at about 160 and being 6'1" it fits me well and isn't as intimidating as a normal height bike.
There's plenty of power for me to putt around the trails with, and I have been able to navigate through tree's and up and down hills just fine with it. The bikes power or weight has not been a hinderance, except maybe when I'm loading and unloading it in my 4x4.
I did replace the exhaust to try and get what ever theoretical power I could out of it and to make the bike a little louder so people would hopefully hear me coming down the trail.
The suspension is similar to an old caddy, so it's a little mushy but it soaks up the bumps pretty well. I haven't done any serous MX type jumps, mostly the water break type stuff. I have to be ready to get jolted as the forks bottom. The rear shock does fine, but I think I can make it a little more stiff, while the front shocks are non-adjustable.
The electric start is one of the best characteristics. Nice to have it when I stall out (my fault) going up some crazy hill.