Tough one. I would want my kids as much as possible, but I wouldn't want to look like I was going out of my way for her either. Personally, I would take them. Of course, if she adheres strictly to the amount of time agreed to, and wants to make up for it later, I guess what's the difference then. Tough one.
Easy one... take them. You're a dad and you're going to show to your kids that you're a great dad and that will never stop regardless if you're married, separated, divorced or whatever with your wife.
With all the change that your wife is introducing to "find her way", you will be the rock for your kids, the protector, provider of security, greatest dad on the planet, etc. Taking them only makes you look good, especially to your kids.
You aren't doing anything for your wife, this is about your kids, you'll always be there for them.
Now when she wants to go out on a date with the OM and asks if you want to watch the kids, that's when you put up the boundary and say that's your busy and you'll watch them when you have them.