I ride a YZ250F, well did but recently sold it to pay off some bills, and I will stand by Yamaha 1000%!! I bought the bike new in 2003 and rode it every weekend super hard (5-10 hours a weekend)..until I sold it last summer. When I bought it I thought I'd be riding the track more but ended up in the woods trail riding. The 250f or 450f is more of a track bike, but with a few mods it can be trail ridden. So that is the first question you'll have to ask yourself, What type of riding will you be doing...track or trail?
I worked at a Honda/Yamaha/Kawasaki dealership for awhile and between the shop guys, sales guys and customer feedback I'd stay away from Honda's 250f or 450f, they are jetted super lean out of the box, require tons of valve adjustments and are a B_tch to start!! Yamaha...hardly any issues followed by Kawi's. Honda does make a very nice trail bike though! The 250x or 450x are very nice and have electric start!! As for Yamaha either bike is awesome YZF or WRF! I'd personally get the WR450F, replace the throttle body stop with the YZF throttle body ($200 swap) as it only pulls half throttle out of the box, and then it is BA after that mod. Also the newer WR's have electric start with a back up kicker, the Honda's don't. The Kawasaki KLX just popped out the FI but as with any first generation FI I'd wait a few seasons to get the kinks worked out. The Kawi's are great bikes, however, I'm not a Kawi guy. KTM makes probably in my opinion the best woods bike on the market, but the price of the bike, parts prices and maintenance schedule pushed me to Yamaha.
To answer the question of cost of maintenance between the 2 stoke and 4 stroke depends how long you are keeping the bike really...you can ride it hard and put it away wet..expect issues in the future, but if you maintain it you could potentially have a great running bike for a long time. After every ride/weekend in my case I'd clean and lube the chain, clean the air filter (key to engine longevity) and change the oil and oil filter. I never had any issues with my 250F and I beat that thing!! Though since the purchase and poor choice of bike for the type of riding I replaced the clutch once in a 5 year period of time but never had any valve issues!!
At the beginning of each new riding season, in the Pacific Northwest that is about March to November, I'd take the bike to my dealer shop to have it tuned, fresh tires mounted and a valve check...really the only thing the tune up is are a new plug, oil change, oil filter change, clean air filter and valve check/adjustment, chain adjustment/cleaning which runs about $200 'ish'. After that I'd maintain it until next year ie oil changes, oil filters, air filters, chains and spark plugs. The cost associated is mainly in oil, oil filters and plugs ($30) as you can reuse the air filter and even the oil filter every other ride. Follow the FSM for exact periodic maintenance. It's nice to have a professional do a once over yearly in my opinion, as I'm not the best mechanic!!
The 2 stroke usually requires replacing the piston and or entire top end yearly depending on the beating you give it. 2 stroke bikes are snappy quick and have a wicked power band and the 4 stroke is constant power all the way thru! I liked riding both 2 and 4 stroke bikes but I would ride a 4 stroke for life!!
Just my .02