I've said it more than once, but I'll say it again,
Feel wise, Ebony, Rosewood and maple are quite different, tonally, the difference is sooooo minimal 99% of people would never notice it.
I have out of curiosity and due to opinions on this very site, taken one guitar neck, on one guitar, and over the course of 2 weeks, changed the board from the original rosewood, to maple, and then to ebony just to see what the difference in tone was.
The actual tonal difference, with a solid body guitar, through a bypassed amp (just the guitar tone) Nothing that I could tell and I have a damn good ear.
The only guitar I think I've noticed a difference on is the Strat maple necks where the fretboard is one piece with the neck, not glued on.
The fretboard is such a minimal piece of wood, and with a GLUE joint between the board and neck to rob any actual chance of tonal variation, that it doesn't not do squat for tone IMO. Your fret size makes a greater difference due to string contact area.
That being said, the subconcious mind will tell you that one or the other sounds better, and, chances are good that if you play 3 different guitars, one maple, one rosewood and one ebony, they will all sound different, but due to many more variables than just the fretboard. If you were to be blindfolded, and play the neck that I had changed the board on, and every board was cleared so there was no difference in feel, I would bet that guitar that nobody would know the difference in tone between the fretboards.
So what guitar did that neck end up on, the JEM911USA with the ebony, why did I choose ebony? I like the feel, and I prefer the look of nice dark ebony.
Anyway, that's just my opinion from an experiment, I know many won't believe me, but whatever, I did it, and it's my educated opinion, I'm sure there is a small tonal difference, but I doubt any human ear would actually notice it.
So, when it comes to picking a fretboard wood, I just suggest going with what you like the feel of the best.
Just my two cents