Well, on the bright side of things, there will be fewer people there. So if she thinks it smells like dirty diapers, then there will be fewer people to create that odor.
You could always bring some room air freshener with you.
We haven't ever stayed at POP, but are going to on our next trip this coming January. It'll just be DH & I and I am looking forward to it. DH tends to be the Negative Nancy between the two of us and will probably not like POP for some of the same reasons he didn't care much for ASMusic last time:
- pretty spread out resort + we ended up in a room far away from main entrance
- lots of loud children (but hello? You're at a Disney resort. This goes without saying)
- room 'felt small' - but we didn't spend a whole lot of time in the room anyway
- food court options were just sort of 'meh'
- bus transportation
BUT...in my opinion, there are some pluses to POP:
- doesn't share bus service with the 3 All Stars resorts
- Skyliner access to Epcot and DHS, so you can sit on your sweaty ride to either of those parks instead of standing on a sweaty bus with lots of other people.

- if you get tired of the food court, I've heard that the AoA food court has some nice options.
- renovated rooms
- we sprung for a preferred room so we'd be closer to main entrance since DH whines about how it is to walk places at WDW sometimes.
That being said, she can look at the glass as half full or half empty. From what I've read, the non-suite rooms at AoA are the farthest away from the main building, so your sister might not have been too happy there. However, maybe she's mostly annoyed because maybe she really wanted to stay in a Moderate but all the 2 of you could afford was a Value.
If it were me, I'd rather stay at a Value than not be able to go to WDW at all.