I will be going to disney for the first time with kids (2 and 5). The way you explained it makes sense, but now I see there is no advantage to the other parent and baby, who would indeed have to wait the 40 min as you pointed out. To avoid such long wait times ( our kids and us don't have patience) me more than anyone else, is there a time where FP ques are not 15 min but just a walk in? would that be early in the mornings?
I am hoping to get FOP FP 60 days out but have read that its impossible to get that ride FP
It varies a lot and there are so many factors that can influence it from how busy the parks are to if the ride has broken down earlier (causing some FP holders from earlier times to be riding with an anytime FP), to how popular of a ride it is, to just sheer luck. A bunch of people might use their FP right ahead of you making the line a bit longer than normal. I imagine FP lines for Kali are shorter on cold days since you usually get wet on the ride. FP lines for Barnstormer are often a walk-on before park close since it's a kiddie coaster and many families with young kids leave the park earlier. Some FP lines can be almost a walk-on, on occasion they can take more than 15 mins, but generally you're probably looking at spending 10 mins in FP lines.
Also remember that some rides will take longer to get through due to pre-shows or long exit queues. Rider swap is not really a quick process when you have to do that twice. Whoever is staying back with the too short kid(s) can do whatever during that time though, like get a snack, use the bathroom, ride something else nearby, go shopping, etc. You don't have to just stand there bored waiting. Use that time to do something else and it helps to pass the time (and can also be an effective use of time if you're doing something needed like a bathroom stop rather than spending more time doing that when everyone's done riding).
Lastly, no body really had endless amounts of patience or wants to wait for things, but that's honestly such a huge part of Disney that you may want to come to terms with it before your trip. You will likely have to wait in lines for the bathroom, for snacks and quick service meals, to be called back after checking in for ADRs, bus lines, lines to get in the park... They're everywhere.
To help make waiting easier for the kids, bring some snacks (goldfish, pretzels, fruit snacks, etc) to occupy them and hold them over when they are hungry. Maybe have a couple of small toys that they can play with, show them pics from the trip on your phone, discuss what they like about various rides/attractions or what they want to do next, play iSpy, look for Hidden Mickeys in lines or point out the little details. My son at 2 was obsessed with the unique light fixtures in many of the queues. Finding something to distract them with often helps with the boredom in lines.