Returning player - what to choose?

[Niwashi]

1] Does the class I start on affect my main storyline or is it the same for all? Unsure if it's linked to race or class or starter area?

Your starting class determines which city you'll begin in, and the first 15 levels of the story are based on that starting city. After that, the stories merge and it no longer matters where you started. And even in those first 15 levels, classes that share the same starting city will have the same main story.

2] What races are there less of and why? I would love to be a less common race if there isn't a snag to that race that others have avoided.

There's lots of Mi'qote and Hyur. Any of the others would probably suit your rarity desire. The only one with a snag I can think of is that Lalafel sometimes have a harder time getting the camera angle where they can see everything easily, just because of their lower vantage point, but you can usually overcome that just by pulling the camera back further.

3] Is it an option to leave gathering/crafting professions until much much later or would that put me at a disadvantage somehow?

The only disadvantage would be that you can't craft your own leveling gear, but plenty of players don't do that anyway. I think it's certainly an option at any rate to do it whenever you choose.