So much depends on suspension set up for you and your preferences. The stock enduro bikes suspension might be closer to what you want offroad, but you are likely to have to modify either to be optimum for you.
The enduro model will probably already have a big tank, which is nice if you like to take long rides. It will also have an 18" rear wheel, which is something you probably would not pay to change if you buy an MX bike.
My old bike was an enduro/crosscountry equipped '99 Honda CR250 I bought from a former district enduro champ. It was like a magazine project bike, with all the trick stuff. The end result was it was a great offroad bike. Gentle as a kitten when crawling through technical terrain, but a real tiger on faster trails. The close ratio gearbox was rarely a problem in the woods, as it had enough motor to pull first gear in even the nastiest stuff. But in the desert, I wanted a 6th gear that was not there.
My current ride is an '02 250 exc with Novation suspension. Like the modified MX bike, it is light and nimble, with plush suspension, good low end and it rips on top.
If you are buying used, it is certainly possible to find an MX bike that has the offroad gear you are looking for. That way you get the goodies and don't have to
pay retail price for them.
Bottom line is a well set up 250 two stroke is tons of fun offroad, even if it started life as an MX bike.