I think it's a bit of a dick move not to invite his nieces but just how close is he to them? If he is not willing to fight to have your children there, from his point of view they are not close. As hard as that is to hear, if he really cared he'd have found a way to ensure they got invited. The same goes for your step siblings, he's allowed to cut them from the guest list if he wants to.
You assumed they'd be flower girls but it may be that the way they are planning he left choice of flower girls to his soon to be wife. If she's close with the girls she's chosen then that's fair enough and is completely up to her. I get that probably stings but this isn't about his partner at all.
My MIL also got quite upset she wasn't hugely involved in planning too, forgetting that she should have her own opportunity with SIL if she'd choose to marry. The assumption was she should be involved but, whilst I spoke about it quite a bit with my mum, she wasn't involved like MIL wanted to be either. It caused a great strain and I nearly called our wedding off.
You're entirely welcome to express how you feel, you're allowed to feel how you want but not every behaviour is justified. Don't make this all about yourselves, don't add a mountain of stress at an already stressful time.
Step back from the emotional attachment to this, attend to see him get married then if you'd like then leave after, you have kids you'd like to get back to after all. Unless you want to burn every bridge there is with him, no one attending from his immediate family would be incredibly hurtful and, to them, justify you all never speaking again.