I love that you plan to name your daughter after your grandmother. In my book, that is always a great idea. Lyn is a beautiful middle name and seems to work with any name. I am used to seeing Lynn so that kind of threw me off a bit.
(Yes! Everyone is used to Lynn. We're just a Lyn family. That's my middle name and my sisters', too.)
For the names -
Adeline is a elegant and beautiful name. It reminds me of that movie The Age of Adaline. I know it's a different spelling, but I still think of that movie.
Charlotte is a timeless name; Charlie is an extremely adorable nickname for a little girl if you want to do that.
I don't think I have ever seen that spelling of Emilee before. I guess Emily would look too tacky with Lyn, though. It's still a pretty cute name. It's a modern day spelling that one can appreciate and is not too over the top like some names out there.
(Thanks to all this! Seems like they're going to work if they don't get vetoed. Emilee is a harder sell because of the spelling, but I like it, and Emily Lyn does just look a bit over ly-y to me!)
Ruby Mae Lyn is beautiful, although, those names are very short together. If you want some contrast, I suggest a longer middle name possibly or having a hyphenated first name instead. Ruby Mae is very pretty, otherwise. I don't know what your last name is. If it's a long surname, it could possibly complement the name. If that's the case, that is a fine name.
(I'll have to think about this one. I haven't come up with any other good Ruby combos! I don't know that the last name really works - it's just two syllable, and also has harder sounds.)
Blair and Sky are cute names on their own, but don't seem to have that "oomph" together that one may want to hear. Once again, there may be that issue with the names being too short. Blair and Sky would be a cute sibset; boy/girl, girl/girl, or boy/boy. That is the beauty of unisex names. I know you only have girls listed here, but I would take that into consideration. You may have completely different rules for boys, so if that's the case, just ignore that suggestion.
(Thanks. I guess the more I say it, the more abrupt it sounds! And I'm not really a unisex kinda girl - except Riley, which I do like for boys, lol. I feel like Blair - or Blaire if I went with that - is a bit different from my other names. Hard to find a pairing that works when you need to have two short names - like Blair and Lyn! Eesh.)
Grace is another Lyn. It works with almost anything. You said you don't like "uh" sounding names. My suggestion is to be careful about picking a name that shares the same sound. Sometimes it works, but otherwise it just sounds too tacky. As long as the name rolls off your tongue, it should be good. How about combining Grace and Lyn? Gracelyn? Sounds like Graceland, which is pretty neat. With this you have the issue of having any future daughters with the middle name Lyn, though. I'm trying to come up with a name that works with Grace, but everything I am thinking of ends in an "uh" sound as that is what I would do for a common name like Grace. Charlotte Grace Lyn would also be adorable. It has the right amount of syllables. It's not too short or long and has a nice contrast. Charlotte is a long name, though.
(Yeah, that's my problem! Grace might just have to be one of those names that doesn't get used but I always admire. )
Some other ideas that may work with Grace - Morgan, Zoe, Adele (kind of fits in with Adeline), Briar (could work with Blair), Chloe, Grace Claire would be cute, Hazel (kind of old-fashioned but making a comeback), Ivy, Lily, and Mabel (another pretty old-fashioned name).
Gwendolyn is beautiful, but I think it's too much with Lyn. I had this same issue with Elena Noelle. They both can be nicknames and both would be Elle for a nickname, which is tacky and doesn't make sense. With Gwendolyn Lyn, both of her names would end in the same name. Gwendolyn at least ends in Lyn, so that could still be a tribute to your grandmother. Gwen is an adorable nickname, and I'm sure your grandmother would be proud if you decide to name your daughter that.
(Perhaps! I really want to stay with the middle name being Lyn. Gweneth, I suppose, or Gwyneth or Guinevere with Gwen as a nickname ...)
You don't have to have a particular theme; I am undoubtedly going to be going through this with my kids. My boys names are mainly classic, biblical-themed; my girls are mainly Italian and Spanish. One is Russian, even. If you love Keira (which is adorable and a guilty pleasure), go for it. Keira Lyn rolls off the tongue quite nicely. Keira Lyn, I would make a double name, personally. It just has that oomph when saying it.
(Yeah, I wish I wasn't such a perfectionist! Keira is kinda a guilty pleasure for me, too!)
I hope some of these suggestions help you out.