Whether it makes a big difference to you depends on several things:
1. Are you someone who must look at the frets when you play in low light - the plastic fretboard is clearly harder to see in low light. Personally, I try not to look, and the plastic fretboard doesn't bother me. If it did, I would put a few drops of white fingernail polish on the side of the plastic as a guide. Alternatively, drill a tiny hole and insert some white plastic as one thread here demonstrated.
2. Do you not like the way the uke looks with the plastic fretboard - again I like the way my all black lava flea looks, especially with the all white Aqulas sort of floating above it.
3. Do you want to play with wound C strings - I don't, so I don't have to worry about that one. I didn't even like the wound C on my tenor before I went to Aquilas.
4. Do you want to play outside and in harsh environments without worrying about it - I do.
5. Do you want to worry about humidity etc. with wood and metal frets - In my short ukulele career (2 1/2 months) I have already had enough experience with popped up frets, bad intonation etc, to last me a lifetime.
Even if they are more worry, I love my wooden fretboard ukes btw, I just also like the utility of the all plastic fretboard, and I like the way it feels, just as much as I like the way my rosewood fretboards feel. It is just different, but I enjoy the Flea for what it is.
My understanding, which may be wrong, is that you can send a Flea/Fluke back and have the fretboard replaced with the wooden one for $85, compared to the $75 more it costs to get one like that in the first place. Of course there would be shipping charges, but its not an irrecoverable decision.