For our first daughter we used a family name for the middle name and we are planning on continuing that trend 
[name_f]My[/name_f] husbands dear grandmothers maiden name was [name_m]Skipper[/name_m], I think it would be a cute middle name for a girl – but our last name is [name_m]Stone[/name_m]. Thoughts on “skipping stones” or do you think it works? Also which of our first names do you love with the middle name [name_m]Skipper[/name_m]?
[name_f]Aria[/name_f]
[name_f]Aurora[/name_f]
[name_f]Aviva[/name_f] ([name_u]Avi[/name_u], [name_f]Viva[/name_f], [name_f]Vivi[/name_f])
[name_f]Jade[/name_f]
[name_f][name_u]Juniper[/name_u][/name_f] ([name_u]June[/name_u])
[name_f][name_u]Saige[/name_u][/name_f]
[name_f]Scarlett[/name_f] ([name_u]Scout[/name_u])
[name_f]Sedona[/name_f] ([name_f]Sadie[/name_f])
[name_f][name_u]Shiloh[/name_u][/name_f] ([name_f]Lolo[/name_f])
[name_f]Soleia[/name_f] (Solie, [name_f]Leia[/name_f])
[name_f][name_u]Skyler[/name_u][/name_f] ([name_u]Skye[/name_u])
[name_f][name_u]Willow[/name_u][/name_f]
I think it’s fine! I think it works with all but [name_u]Juniper[/name_u] (the repeated ipper sound with [name_m]Skipper[/name_m] is too much), [name_f]Scarlett[/name_f] and [name_u]Skye[/name_u] (both names having the sk sound).
Ok idk if this is too much but I kind of love the idea of [name_f]Scarlett[/name_f] [name_m]Skipper[/name_m] [name_m]Stone[/name_m] “[name_u]Scout[/name_u]” or [name_u]Skyler[/name_u] [name_m]Skipper[/name_m] [name_m]Stone[/name_m] “[name_u]Skye[/name_u]” kind of sound like character names but in a wearable way
[name_f]Sedona[/name_f] and Solaia are my favorites from your list.
The [name_m]Skipper[/name_m] and [name_m]Stone[/name_m] doesn’t bother me - if anything it has a nice imagery!
I think [name_m]Skipper[/name_m] is adorable as a middle! As for the association, I’m not sure it’s ideal but it is a sweet image and middle names aren’t used very often.
For your first names, I love all of the A names you picked out but I would eliminate them because with [name_m]Skipper[/name_m], her initials would spell “ASS”. [name_f]Scarlett[/name_f] [name_m]Skipper[/name_m] is so sweet, and I like [name_u]Shiloh[/name_u] [name_m]Skipper[/name_m] as well!
[name_f]Scarlett[/name_f] [name_m]Skipper[/name_m] [name_m]Stone[/name_m]!
I think [name_m]Skipper[/name_m] is fine with your surname. What a fun family name to have!
[name_f]Aria[/name_f] [name_m]Skipper[/name_m]
[name_f]Aurora[/name_f] [name_m]Skipper[/name_m]
[name_f]Aviva[/name_f] [name_m]Skipper[/name_m]
[name_u]Willow[/name_u] [name_m]Skipper[/name_m]
These four sound the best to me with the middle name and surname.
I notice you seem to really like S names, and I generally like alliteration, but three S names in a row is a little too much to my ear.
I hadn’t thought of this, but I think my vote goes to [name_u]Willow[/name_u], for this reason. [name_u]Willow[/name_u] [name_m]Skipper[/name_m] [name_m]Stone[/name_m] would be fabulous!
It works just fine in my opinion. I was actually thinking about [name_m]Skipper[/name_m] the other day, it’s such a fun, offbeat name. I think [name_u]Willow[/name_u] [name_m]Skipper[/name_m] would be especially lovely! 
I think it would be a bit much for a first name, but it’s cute as an MN.
I like [name_u]Willow[/name_u] [name_m]Skipper[/name_m] [name_m]Stone[/name_m]!
I think it’s fine… as long as you don’t use an S first name. [name_u]Juniper[/name_u] [name_m]Skipper[/name_m] sounds perfectly fine!