A 40hp MC28 should be reliable as the day is long, so don't be put off by the fact it's a 2-stroke. I have NEVER owned anything but 2-strokes, and properly looked after there is no reason why they won't go on and on. Yes, they can seem to be more unreliable, but it's the nature of the motor. It fires on every TDC (twice as much as a 4-stroke) and is capable of making well in excess of double the power of a comparatively sized 4-stroke. Ask a 1994 Fireblade to make 240bhp/litre* and see how long it lasts! 240bhp/ltr is what just a "delimited" 250 will make, not even a tuned one, and is why they are more labour intensive.
Tens of thousands of 40 and 45hp 250 2-strokes were daily rides for commuters and leisure riders in Japan, and were among the most popular bikes on the road for 15 years, not without reason. There's not even a lot to look after. Keep the air filter clean, change the spark plugs every few thousand miles, and use the best oil (not that most commuters would even have done that back in the day!), and there's no reason why ANY Jap' spec (40~45hp) 250 won't do 40~60,000 fairly trouble-free K's.
People telling you they are unreliable are often trying to screw big horsepower out of them, or maybe even mediocre HP and either just don't know how to set them up, or don't service them regularly considering the increased performance! Simply following Honda's standard maintenance schedule for a tuned 65hp NSR for example, isn't a good practice. The Workshop Manual/service schedule is based on a standard 40/45hp bike, not a delimited one making over 60hp... doesn't take a rocket scientist to work out it will need additional care when making 50% more power. Not only does it make that additional 50%, but it will probably be ridden even harder given the increase in performance.
Buy a low mileage, standard bike, and get an official Honda Dealer to service the top-end. It's just as likely to go wrong as any similarly abused 250 or 400 learner 4-stroke probably!
Everyone here needs to consider how wrecked any of their learner bike experiences are/were! Nature of the beast! Cheap and cheerful bikes for cheap and cheerful "yoofs"! If you want a mint, reliable bike, buy a new VFR800! If you want something suicidally fast, buy a new GSX-R1000, if you want cheap, simple, fairly economical fun, buy a 15 year old 250 or 400, but expect to have to look after it, or fix some stuff from time-to-time! 
*According to Honda, a standard 124hp 1994 Fireblade makes around 138.86hp/litre -- a standard 40hp MC28 makes 160hp/litre. You are also asking 40hp to cart around 60~100kg of rider + kit... of course it's going to have a harder, more stressed, more labour intensive life.
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Andy.
NSR-WORLD.COM
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