Full timers get room priority.  With toddlers the room closest to  the the adults room can be the nursery regardless of  room size until the LOs get big enough to have a bed.  Then start looking at shifting the full timers to the bigger rooms as is age appropriate for the 100%ers.

KISS. Keep It Stupid Simple.

Don't let emotion cloud judgment in making decisions that are best for the full timers.  Anyone's emotion that is.  The 25%ers get where they fit in the way that minimizes overall household interference.  Since they are on opposite schedules one room will suffice for both of them to share since only one is there at a time. The 50%er gets more consideration regarding a dedicated room than do the 25%ers.  
 

IMHO

In my mind those who share the room get the larger room.  The littles should be close to Mom and Dad.  I think your first set up is perfect, but your down the road one may not be.  I'm not sure that an 10 year old should be in a room with a sliding door for 6 years until the 12 year old moves out.  The 3 year old until 9 seems like a better fit for that.  Unless you're willing to bite the bullet and turn it into a proper room with a proper door, I wouldn't put a teenager (10-16) of either gender into a room with little privacy over a 3 -9 year old. Perhaps you ask the child at that time.  Do you want the smaller room upstairs or the rooom away from mom and dad but without a door.  Your little will have pick of their rooms as soon as she is gone.

it's more than age that dictates.  clearly smaller kids can share barring issues with them "getting along"..  the schedules matter too and having kids who are on opposite schedules share a room when there could be occasional overlap is fine.. .

I would also be liable to want more sharing with one room being more of a "play room"/guest room  that was the set up for my brother and I untl I was 12 (he was younger).  we shared a room but had a room where we could play.. watch TV.. but was also a guest room occasionally.  

sharing a room has lots of benefits.. kids learn cooperation.. they can have comfort and camraderie with their siblings (bio or not).. but if there are concerns with over the top bullying.. great age difference.. (more than 5 years)... it may not be as good of a solution.  

I would also want the youngest to be closer to parents.. for ease because they will need more immediate access than the older kids would

You are the queen of the house.  You do wgat ever is easier for you.  3 month and 9 months??? living with you full time gets the easier space where you can take care of them. 

Full-time should dictate room size and location and trump age.

We have 4 bedrooms upstairs, all relatively the same size. I decided when choosing the "nursery" before DS3 was even born that his room should be closest to the bathroom and laundry room. Newborns = lots of laundry. I also did not want DS having to walk past stairs to use the bathroom once he got to his toddler years. 

Of course at the time SD14 felt slighted and "wasn't fair". I did not even consider prioritizng her location because she is not even here 50% of the time.