Well... I have only played two rpg's on my 3ds... So my list is:

1. Fire Emblem:awakening

And that's it. The other rpg I played was bravely default, which is the worst game I have ever played and does not deserve to be a part of any top ranking from me, even if it is from lack of choices...

Really? Yikes. I wish I had the luck of Bravely Default being the worst game I've ever played. In my opinion it perfected the classic FF formula (FF 1-3,FF 5) with a decent enough fantasy story. I mean it's a lot better than Final Fantasy 5 for example, and that was the game which did the job system the best. So 1-3 are definitely worse than it too. 

I have to disagree there; while BD didn't handhold the player (FF6 and on), it was particularly challenging. It also takes a serious hit for making to replay the same thing for the second half of the game. BD is great, but it's value is diminished by its reliance on repetition and the numbered series (especially PS1 and earlier) are an improper comparison. If anything, it's like a shorter, extremely polished version of FFIII.

What are you disagreeing with exactly? You feel it is a polished version of FFIII, which is kind of what I said, although I compared it more to FF5. Also FFIII is only 20-30 hours long, Bravely Default is like 50-60 hours. Even if we exclude the last few episodes (which were repetitive) there is still more than half of the game which is unique. So it's longer than FFIII. 

Final Fantasy III

http://howlongtobeat.com/game.php?id=3496

Bravely Default

http://howlongtobeat.com/game.php?id=1307

The game is essentially FF5, but harder and with a more convoluted story. The job system was better in this game than it was in any Final Fantasy.

the bolder part I strongly disagree with.  Bravely defaults story is just plain bad.  The characters are just annoying cliches and the dialogue is cringeworthy.  The gameplay is competent, but if every time I encounter exposition I feel the need to throw my 3ds against the wall... It doesn't balance out.  

The worst part is I bought the game digitally because best buy had cards for sale... So I couldn't even trade the game in... I am stuck with it...

Everything must be taken in context however. Besides FF4 and FF6, Bravely Default's story is superior to the games it was taking from (Four Heroes of Light, FF 5, FF 1-3.) The characters were meant to be archetypes, but at the same time they weren't overly serious like FF 1-3/FF 5 characters. It was almost a joke on the simplicity of the stories found in JRPG's during that time. I do have to say that some of the voice actors, especially Agnes' were horrible though. This entire game is suppose to be a throwback game to fans of the classic Final Fantasy games. The gameplay was the best combination of the job system with strategy that has been achieved. The difficulty was also refreshing in an era when most JRPG's are a breeze to go through. Additonally, the added choices of reduced random encounters (and other similar features) streamlined the experience.

1. Fire Emblem Awakening
2. Bravely Default
3. Shin Megmai Tensei: Devil Survivor Overclocked
4. Pokemon X/Y
5. Pokemon Alpha/Omega
6. Tales of Abyss

(Xenoblade and SMT 4 will eventually be on this list somewhere).

When comparing them, BD takes a hit for making the whole second half of the game the first half over-and-owver again like 7 times. No numbered FF had that kind of "filler" to artificially lengthen the game. I compare it more to FFIII than FFV, because FFV was WAY more expansive than FFIII or BD: the game had three, distinct worlds that you explore (including the submarine locations). While I genuinely appreciate BD's hat tip to old school FFs (which we need more of, honestly), I can't put it on their level. It's also not that fair to compare a 3DS game to those that were on the SF, but you are right on the difficulty aspect: FFV was probably the last challenging FF, until FFX and FFXIII.

Agnes' voice = super ugh

I guess it is a matter of breadth vs. depth for me. Sure, FFV felt like a broader game, but at the same time the places didn't feel like they had the same amount of depth and detail (like you said though it is unfair to compare the NES/SNES FF games to a 3DS game) as in Bravely Default. Each Bravely Default location felt unique and had a breath of life to it. The socio-politics of the story, while cliched at this point, were also much more interesting than anything in FF3/FF5. There was a lot to do that felt rewarding as well. I had a lot of fun collecting optional jobs and summons through bosses. I didn't really mind the second half too much either, because it was fun to use different job combinations that weren't available before on the same bosses. Sure it would've been better if the world were larger, but I felt like there was more to do in Bravely Default than in old school FF's. The battle system was a huge upgrade over FFIII and a moderate upgrade over FFV. The music was equally as good. And I mean in Bravely Default you always have options to end earlier at certain points in time, so the second half is avoidable to an extent. It's not like the true ending is that great and you can always watch it online. 

"Agnes' voice = super ugh"

Agreed. I searched the voice actress, and aparently she does a lot of anime dubs and is well liked. I don't know how that is the case though. I read a comment, "her voice sounds like a man trying to imitate a woman." And I agree 100% lol.