I said this several times before the wipe, and I will say it again: Skye is an assassin. She should be able to get the drop on you and kill you with the element of surprise. That being said, her ult is absolutely ridiculous.
Combine that ultimate with Evie's and you have full point-clearing with 2 champions.
If, now hear me out, the enemy team happens to not have a Grover or a Fernando. If they do, then you just wasted your ult because they both counter those ults, and they're both good outside of those situations anyways.
EDIT:FeelsBadMan when you post too late and someone already states your idea.
I have not tried the new burn card upgrades, but without it she must be really close to see her, almost contact distance. She could just pass running in front of everyone and no one would notice her.
Casting a shadow would force her use the map wisely instead of just run trought the middle. And, if she gets invisible in your face, she wouldn't be able to just stand there waiting for a chance to finish you.
At the ridiculous uptime Skye and Evie have, Fernando will negate the combo at most 2 times in the entire game, given that his team doesn't need his ultimate to stay on the point outside of Skye's ulti. I thought that Fernando will counter Skye's ultimate too, until I got 45% faster ultimate item on her and after using ulti, I got another ultimate at most 2 minutes later. Fernando as well as Grover need to survive to be useful, so they don't really have the luxury to get lvl 3 ulti reduction, when they need defence cards. I love playing Skye, she's really fun, but the ultimate does need a rework.
Just play for a month or so, you'll be going: Skye? Who's that?