I think we are pretty settled on the name Madeline/Madelyn, etc.  It meets all of our criteria.  It is a nice name, not too popular, and can be shortened to a natural, stand-alone nickname (we like that, and both of our older 2 kids have names like this as well).  
I do like the spelling, Madeline, because of its simplicity, but I do not want it pronounced Mad-ah- LINE.  I am not generally one for a random "y" in a name, BUT Madelyn IS a legitimate spelling, and it DOES convey the pronunciation we are going for.  The French spelling is out for us because it is just too many vowels and can be pronounced differently than we are intending.
I know the different variations of this name's spelling have been discussed a million times already, but we are also now considering Madelaine (Mad-ah-lane) which is obviously pronounced differently than the 2 other variations mentioned.  This may be nice considering all of the Madison's with nn Maddie out there right now.
So... I ask you ladies.
Madeline (nn Maddie)
Madelyn (nn Maddie)
or 
Madelaine (nn Lainie, or Maddie, I guess)
                 
                
Re: Help us decide, girl name & spelling please :)
mm 2/17/11 * dd born 4/20/12 * bo 1/3/14 * edd 1/21/ 1/15
*Siggy Warning*
About me 2007: Started TTC. 2008: OB prescribed clomid, went to RE and was Dx with PCOS. 2009: IUI #1 w/follitsim and trigger = BFP. B/G Twins born at 33 weeks. 2012: TTC #3, Round 2 of Letrozole w/TI = BFP, missed m/c at 8 1/2 wks. Currently on the bench as we make plans for a new home. Anxious to start TTC #3 within the next year!
I realize you've settled, but if your criteria is includes "not too popular" you might want to check the rankings in your state because I know about 25 little Madelines/Madelyns/etc. And more Maddy's than I care to count.
That said, much prefer Madeleine or Madeline. As PP said, Madelyn reads to me as "Made-Lyn"
That said - to me it's a popular name. I know two close friends/relatives with Madelines plus some girls named Madeline (various spellings) at DD's school. (Also a zillion Madisons who might or might not go by Maddie.) I live in DC but I know Madelines in other parts of the country. Just be aware of its local popularity and whether it's trending upward, and realize that a name that isn't wildly popular now can be on the rise and might be everywhere by the time your DD's in school.
Precious baby boy "HC" born May 2013.
With either pronunciation I still think the Madeline spelling looks nicer.
TTC #1: February 1, 2014
BFP #1: 2/21/14 EDD: 10/31/14 MMC: discovered 3/31/14 (blighted ovum) D&C: 4/3/14 at 9w6d
BFP #2:12/18/14 EDD: 8/27/14 Beta #1 (16 DPO): 50 Beta #2 (18 DPO): 54 CP: 12/25/14 at 5w0d
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Formally LisaG09
"Everybody wants to be happy. Nobody wants to feel pain but you can't have a rainbow without the rain."
Thank you to everyone else for your input! I appreciate it and have a lot to think over.
Married 1/2/99.
TTC since 4/09.
Diagnosed PCOS. Diagnosed Hypothryoid 11/09.
SHG & SA normal. PCOS Research study started 5/10.
Clomid/Femara cycle #1 - 6/10 = BFN
Clomid/Femara cycle #2 - 7/10 = BFP #1 - Missed miscarriage 9/2/10
11/12 - BFP #2 - 11/22 - m/c
5/1/11 - BFP #3 - Pre-eclampsia, IUGR & bed rest from 32w. DD born via induction 1/4/12.
https://www.behindthename.com/name/madeleine
Precious baby boy "HC" born May 2013.
Precious baby boy "HC" born May 2013.
I also spelled it this way to avoid the "-line" pronunciation. This spelling never gets much love on this board.
I will add though, that since naming DD (Nov. 2012) I have seen what feels like a 100 Madelyn/Madelynn/Madelines. So I definitely think it has moved up in popularity. It being unpopular was one of my main reasons for also choosing this name, but I swear I hear and see it all the time now. Such a bummer.
Good luck!