Your choices mostly center around deciding what version of plastics and decals you like the best - and whether you like the look of your front forks plain or anodized. Somebody here will jump in any moment with a link to one of our members who has taken the time to track down the miniscule changes between years. Browse it at your leisure - it's a short list.
The biggest thing, probably, is that the Feb/March versions of the first year '08 model had a blip of fuel pump failures. We probably saw about 16 reports in all between this site, ADV, TT, etc. Most of us with bikes in that range have not had a problem, but it certainly is an elevated possibility with those two months. Most who pushed the issue got their pumps replaced by Yamaha; some got them replaced before they had an issue.
Other than that... oh, there was a rubber sound dampening ring on the stock '08 sprockies that disappeared the next year.
We don't believe in change here at WR250R land...