(From a Miss Fortune main/G5~ MMR) Not missing anything. Miss Fortune is a Lane Bully early on, and the rework made her better at it. She's also a great roaming ADC. She's good at pretty much any point in the game. She's no hyper carry, but she should never be underestimated. Not really sure where to start, so I'll just go over her abilities a bit and how to play around them. - Something to note: All ADCs are super reliant on positioning, and Miss Fortune is no exception (possibly even more reliant)
Passive - Strut - It's almost a Boots of Mobility passive, but is only disabled on damage taken (rework made it so that if she has a shield, taking damage to that WON'T break her passive). It caps out at 70 movement speed. Early on, it makes it rather difficult to land a skillshot on a skilled MF player. Hitting her with non-DoT damage will disable the passive for a time. This is her only mobility skill and losing that if being engaged upon can be very costly. See W and E for more info
Q - Double Up - MF shoots a bullet at a target, which then ricochets onto another target behind the first. The second shot deals more damage than the first, making it more rewarding to land the second shot. The second shot is what makes Miss Fortune a lane bully, and the rework increased it further: If the bullet kills the first target, then the second target will take 150% damage from the second shot. Both shots apply on-hit effects (auto attacks) To get around it, you need to be moving constantly to a position where she can't ricochet the first shot onto you (or at least not behind a killable minion). She can always try and hit you with the first bullet, but it does not deal nearly the same amount of damage. She will always max this first.
W - Impure Shots - Has two components: a passive and an active. The passive gives 6% of her total AD as bonus magic damage on each auto attack, stacking up to 5 times for 30% AD added as magic damage (each rank in her ult adds one to the stack limit.). This part lets her deal some nice hybrid damage as well as rewards her for continuing a fight (similar to Vayne's Silver Bolts). Not much you can do to avoid this other than not getting hit by her auto attacks, Double Up, or ultimate. The active grants her bonus attack speed for a period of time as well as immediately activating her Strut passive giving her a full stack. Not much to do other than bait it out, and hitting her again to disable her Strut passive again. She will almost always max this second.
E - Make it Rain - MF shoots a rain of bullets over an area, dealing some damage over time and slowing targets in the area of effect. Used mostly for the slow, it is her only disengage skill (assuming she lost passive). At the same time, it also gives her some decent chasing potential. The rework made it a better 1 point skill by increasing the slow strength (though the duration was reduced a bit.)_ As any other constant AoE effect, simply move out of it to avoid the slow.
R - Bullet Time - MF stops and shoots multiple waves of bullets in a cone shaped AoE. Each bullet applies a stack of her Impure Shots passive. While the initial damage isn't too harsh, stay too long in the AoE and it will devastate you._ Get out as soon as possible (or kill/CC her ASAP.)
TL;DR - Move constantly to avoid her lining up a Double Up ricochet shot and avoid extended fights with her. To my knowledge, Miss Fortune does counter Vayne due to being a lane bully early game where Vayne is arguably her weakest. It's definitely possible to win this matchup, but MF has the advantage.
