They are puppies.
It's not necessarily what's convenient for us as owners, as it is for
what kind of commitment we make when we decided to get a puppy.......knowing what a 'joy' some parts of raising them can be.
Don't blame it on the breeder or what kind of job they did raising the litter. We had the opportunity to choose what environment they come from - live with your choice. It's YOUR puppy now - and they depend on you to make the right choices.
Yes, puppy bladders (and stomachs) are small. They will not be on your schedule.......until they get 'bigger'. If you try to make their metabolic functions fit-in with your schedule, it could cause physical problems or bad habits hard to correct. You reap what you sow.
If you can't tend to the pup when he needs it, then you might need an outside kennel......otherwise, realize that the crate is just a space to contain whatever you don't want to deal with while you were living YOUR life.......and deal with the consequences.
I would only limit water intake in the evening, when they will be crated in the house all night......if you expect to get any sleep and don't want to clean-out wet bedding. Otherwise, my pup has free access to as much water as he wants.....when HE NEEDS it. It's MY responsibility to take him outside periodically to make sure he associates 'outside' (grass) with a place to do his business......not the mexican tile floor or carpet.
About whining: That can be tough if you have one that just wants to be a big baby. Whining should ideally be communication that something is wrong and they would like some help. But sometimes they just want what they want......like ....."outside this damn crate". Think about how much time they spend in the crate and see if that's the kinda life you'd want.
Finally - the whining thing is part of raising a pup. Be thankful you've made some progress in that regard - it could be a whole lot worse. I have not slept a whole night through since August 8th.......and average maybe 6 hours of restful sleep per night (after raising and placing pups @ 7 weeks). But that was the choice we made when we had the litter, decided to keep 2

.....and deal with whatever that brings in the first 2 years of THEIR development. It's just tougher, sometimes.
I have one that has some separation anxiety issues that we are working through. How you deal with that is similar to what kinds of problems you might face (and deal with) in other aspects of training your gun or test dog. He shows enough GOOD qualities that I can deal with the Bad ones (hopefully temporary).
I'm new at this, but thought I'd share some of the things I've had direct experience with.....in the last 3 months, myself.
They are puppies......not video games.