I could be the step mum in this situation, sounds to me like he's doing a fantastic job at maintaining his relationship with his children, and trying to keep everyone happy.
My dh and I have had the suggestion that he should stay at his parents with ss, the reality is that they live in a tiny bungalow, both have health issues and they already have his adult sister at home, it would be overcrowded and unfair to put on them.
From my perspective, and being completely honest, I would also feel that my children (the youngest of which is my husbands and a half sibling to ss) and I were being excluded and pushed out from my husbands family if he were to go swanning off eow, perhaps that is selfish but it is how I'd feel. I also think the children would resent it and feel ss is getting preferential treatment.
When a new partner and children come along things change and everyone has to adapt. It sounds as though you are having difficulty with this and projecting it into something else if I'm being honest. Perhaps if your children were staying at his parents or sisters they would feel excluded and pushed out from their Dad's new family?
I often pop along on journeys with my husband, and it has nothing to do with the fact I think he's going to jump his ex wife's bones the minute my back is turned! It means I, and the children, get to visit dh's family (who are also mine and the children's family), we get to visit friends and we can share the journey, which when it is 7 hours long in our case is a godsend.
It's also worth bearing in mind that although every other weekend may not sound like a lot of time for him to be away from his new family to you, the reality for them may be very different. When you take into account working hours and other commitments they may get very little time together as a family themselves, in my case uni, work and other children's commitments leave us with very little time together, as family or couple!
You may not think of a car journey as quality time, but we've found that the best conversations seem to happen when we are stuck in a confined space with not much to do, we often stop for a meal out too. I'm sure if the journey was problematic for your children they'd let you know.
Regarding the assuption that because she has no relationship with her ex she thinks yours and your exes relationship should be the same, I find it hard to believe that's her mindset. I have no relationship with my ex and the last thing I think about my husband and his ex wife is that their situation should be the same. I want anything but that after seeing the upset caused to my son and would never want ss to go through that.
You don't say much about your relationship with his new partner, but assuming she isn't the other woman theres no reason you can't invite your ex and her in for a coffee to chat about the boys. I know there's a general consensus that the ex and new partner don't need to have any kind of relationship, and they dont, but its much better for children to see the adults getting along, and will make other circumstances where you're forced to be in her vicinity less awkward.
It sounds like they are both trying their best to build a family where everyone feels valued and included. I think you are very lucky to be honest. There's no reason his partner has to be seen of as the enemy (unless she's the OW, in which case I'd understand the hostility!) you never know what may happen in the future, maybe they'll move closer or the boys will decide they don't want to do the journey so often. In the meantime you just have to make the best of it and appreciate the fact they are trying their best to act in everyone's best interests. As well as being in the other woman's shoes on this post I also know what it's like to witness your child being abandoned and pushed out in favour of the new family, I wouldn't wish that on anyone.