In my experience, sand teams have come up more often than rain by a long shot, although rain teams are still quite common.
To answer the question of genesect's best set, I've got to say it comes down to your team and what it needs. mostwanted's sashsect is extremely effective due to its coverage and ability to switch between moves, while focus sash lets it beat scarfsect and serve as an emergency security measure. However, scarf genesect is generally easier to fit onto teams and serves as a great revenge killer and lead. I use scarf genesect on my current team, but have used sash in the past.
In reality, flame charge is probably an inferior option in general, although it has its uses. Running flame charge over flamethrower lets genesect come in on something weak to fire, force it out or kill it with flame charge, and then hopefully sweep with +1 speed and the ability to switch moves. Check out shakeitup's DW RMT if you're interested: http://www.smogon.com/forums/showthread.php?t=3465631
For chandelure, I would again say there is no "better" answer, but that modest is generally more useful for the extra KOs. On the other hand, if your team has trouble with dragonite and scarfmamoswine (or something like that), timid will fit your team better.
This is just personal experience, but I find that well-executed rain stall teams are some of the most potent out there. As mostwanted said, these (almost) always have politoed, tentacruel, skarm, chansey, and the like. It is true that such teams have a fairly mechanical play-style, but they can be very effective.