The biggest single concern in the difference between a maple and rosewood fingerboard is the cost of maintenance down the road. There IS a very real - and noticeable - sound difference, and that is also of concern.
Maple boards tend to be brighter, and noticeably so. Rosewood fingerboards are therefore, of course, warmer. Ebony fingerboards are brighter than rosewood, but warmer than maple. These differences are quite noticeable on an electric, but on an acoustic they become negligible because so much of the kinetic energy is lost in the vibration of the top (in particular) and the body (in general).
Maple fingerboards, however, have one major disadvantage. If you want the guitar to last your lifetime, they must be protected by a hard finish. They simply MUST. Without it, you are looking at shortening your guitars useable life to less than ten years, even if you play infrequently. Maple is simply too vulnerable to finger oils and environmental humidity changes. This finish leads to several problems. First of all, if you play at all, you will eventually need your frets dressed. This is quite a bit more expensive on a maple fingerboard, simply because the finish is a lot more delicate than on a rosewood fingerboard, and so it takes greater effort to avoid marring it. Second, if you keep the guitar for a long enough time, you are going to need a refret. This requires refinishing at lest the face of the fingerboard. It turns a $300 refret into a $400-500 refret. In most cases, it makes more sense to replace the neck than to refret them, but unless you get one of the few guitars which Fender regularly sells, you will not be able to get an exact replacement, as Fender has recently stopped selling replacement necks. The only time they send out exact replacement necks is on warranty work. They have always been a bit stingy with their exact replacement necks, but they have gotten much more so. Because of this, you are getting a neck from someone like Warmoth, and while there are companies whose quality is at least a match for Fenders, it is illegal for anyone to put a Fender decal on them, so you are looking at a blank peghead guitar (if that matters to you, and it matters a lot to some people.)
Personally, I like rosewood boards on Strats.
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