I personally like Ryanne better than either Rilynn or Rylinn. Yes, there may be some confusion about whether it's pronounced Rye-anne or Ryan, but I think the pronunciation/spelling will be questionable with all of these choices. Ryanne seems a lot more straight-forward to me. Just say "we pronounce it ___."
If you're open to other suggestions, I have known little girls named Rylee and Ryne. Both of those sound more like they're honoring the name Ryan to me than Rilynn/Rylinn. I have also known a number of little boys named Rylan and Ryland, so I wouldn't go that route.
Alternatively, I really like the suggestion made by a previous poster to use Ryan as a middle name. With a more feminine first name, I think a masculine middle name can sound really spunky and charming, and gives the girl another option if she turns out to be a tom-boy.
also, When I hear the name Rylinn/ Rilynn it sounds more feminine to me. When I think of that name I think of the name Kaylinn too, which I really like. And it reminds me of other names ending in -linn/ lynn. I think Rylinn is a great name, and I like that its unique. And if you are honoring a Ryan, any names starting with Ry (whether it is a first or middle name) sound perfect for that!
Oooo! This name has really got me thinking now. Rylinn, Rilynn, hmmm something about it. Anyways, have you considered the spelling "Rylan" or "Raelyn?" I'm not sure if you would think of Rylan as a boy spelling or not, but I think it's cute. Raelyn: I guess it would depend where you're from because some people might say "Rae-lyn" rather than "Ry-lyn."
As for middle names, I like Rylinn Cecilia, Rylinn Lorrain, Rylinn Michelle, and Rylinn Margot.
I think both Rylinn and Rilynn look like they should be pronounced like RYE-linn, almost like a double barreled first name. The suggestion of Rylan makes more sense to me. Or maybe Rylane?
What about some names that incorporate some of the sounds in your brother's name? Like Roxane, Rosanne, Maya or Riley? I know you've said that your brother liked birds, so what about something like Roxane Lark or Rowan Sparrow? Or what about Robin? Robin Cecelia is a beautiful name.
Rylan ranked at #179 for boys in 2012. There were three times as many little boy Rylans (2158) born as there were little boy Archers (714). I'm a Southerner too, and the two Rylans I've met both pronounce the name just like "RY-lyn." Your daughter Rylann (or however you choose to spell it) has a much better chance of sharing her name with her male peers than your son ever will.
I don't have any suggestions for you. In your shoes, I would use Ryan as a middle name; I would like the direct, unaltered, undiluted connection to my brother's name, and...well, I've always liked masculine names like Ryan, Brett, and Drew as middle names for long, formal, feminine names like Elizabeth, Beatrice, or Cordelia. It would work for me. Naturally, you'll have to do what works for you. I hope you find the perfect name, one that strikes the right balance between appealing to your tastes and satisfying your need to honor your brother.
Do you like Rhiannon at all? I know it doesn't have 6 letters, but I think it's fairly evocative of Ryan in sound & appearance, and it has the same meaning (queen/king). And it is clearly a girl's name, if you are at all concerned about that. I also like one of the other posters' suggestion of Riley or Reilly!
That being said, I agree with everyone that you should choose whatever you like best and whatever you think is the best tribute to your brother Ryan. I like Rylan a lot, though I have seen quite a few boy babies named that lately. I like Rylinn and Rilynn equally, but I would pronounce them both as RY-lin. Not sure if you wanted a ry-LYNN sound or not? The thing is, at least to me, Rylinn, Rilynn, Rylan, and even Ryland are all going to sound pretty much the same when spoken. Rylinn & Rilynn are both clearly "girly" when written, whereas the other 2 look more unisex. Just food for thought; I don't think of anything I brought up as a problem or reason not to use the name!