Because about 90% of the game is awesome.  The ending sequence was creative and interesting even if it didn't work that well, and even if you call it padding, the game still had plenty of content.  Best turn based battle system in years, one of the better JRPG stories, and very creative use of street/spotpass. 

I wouldnt agree that any part of the games was good except maybe the battle system.  The characters were cliche and forgetablle, story was boring and predictable.  Even the battle system could have been a lot better.  The job system was just wasted potential.  And then there is the padding...

no, I would not recommend the game to anybody.  If you enjoyed it, more power to you.  Just know what message you are sending to developers by supporting it.  Skimp on story and pad the gameplay and your game will sell...

Senran Kagura Burst is a good brawler (and one that makes good use of the 3D function). Bravely Default is a very good JRPG, Pokémon X and Y are good games, Star Fox 64 3D is a good rail shooter (albeit a bit short). Monster Hunter 3 Ultimate is a good grinding RPG (but you'd better have the Circle Pad Pro attachment for that one). There are a lot of good indie games worth checking on the e-Shop. Fire Emblem: Awakening is a good grid turn-based JRPG. The Legend of Zelda: A Link Between Worlds is well, a Zelda game (worth checking out). And on and on... The 3DS has quite a large game library.

Pretty much.   There is a reason why nobody claims ff 1-3 as the best games in the series...

I can only recommend games I've played so here they are:
Fire Emblem Awakening
Zelda OoT
Kingdom Hearts 3D
Tales of the Abyss

Well my Top 5 would be:
1. Luigis Mansion: Dark Moon
2. Pokemon X / Y
3. Mario Kart 7
4.Fire Emblem Awakening
5. Bravely Default

The whole point of the game was to be a throwback to early FF.  Complaining that you didn't like this because it was too much like early FF is like complaining that you don't like COD because there's too much shooting.

thats a terrible analogy.  A more apt analogy would be it is like complaining that COD is too much like wolfenstein (or goldeneye, or some other early fps).  Fact is, the RPG genre has progressed in last 25 years since the early FF games came out.  

Now, I loved playing goldeneye back in the day.  I played it non stop with my buddies for years.  However, I tried to play it a couple months ago and guess what, it is garbage now.  It has not aged well.  

Bravely could have easily served as a throwback to early FF games and still integrated a decent story with interesting characters and without using the gameplay padding scenario.  The battle system was good, they just failed in everything else they did. 

This. I found the story engaging, and loved the battle system. I actually enjoyed grinding for once!

Also agreed on the ending sequence. I braced myself for Chapters 5-8, and actually didn't think it was as horrible as some people made it out to be. It could have been improved, no doubt, but it was creative enough to keep me attached, and certain plot points had me coming back for the whole sequence. Though I do hope it's done a bit differently in Bravely Second, it also wasn't a turn-off for me.

@OP: I'm probably gonna miss a lot, but my personal favorites are:

Fire Emblem: Awakening

Tales of the Abyss

Bravely Default

Shin Megami Tensei IV

Zelda: A Link Between Worlds

Kid Icarus: Uprising

Mario Kart 7

Past that, if you wanna play some remakes, Ocarina of Time 3D and Star Fox 3D are both a lot of fun. Also Pokemon...if you're into that.