Wow, what a daunting list of games to choose from

! Out of those 5 games I own 4. I have beaten 3 (Days of Ruin, TWEWY, and 999) and am currently playing Radiant Historia. They are all really different games, despite more than half being rpgs. If you are looking for something to play along with something else on your 3DS, I'd pick Days of Ruin as it will require I think the least amount of attention (being least reliant on story of the bunch) and as a game that can literally be played turn by turn.
If you want something short but punchy, I say go with 999. The first play through will arguably be your longest, but even that's at most maybe 4-5 hours or so ( it's been a while since I played through it). If you like what you played by your first ending, you can go through it again to see alternate paths to the game and ultimately flesh the story out more to it's awesomely satisfying conclusion. If you don't like it by your first ending, you can put it down satisfied that you at least *beat* the game and can can clear it from your backlog without guilt.
If you are looking to really lose yourself in a setting/story and really dig in, then I recommend either TWEWY or Radiant Historia as both cannot be really played casually because of each game's relative complexity (both combat and story wise). Of the 2, if you find using the stylus a lot for combat in a game fatiguing or uncomfortable, play Radiant Historia.
Otherwise, play TWEWY as it will be a brand new experience to you unlike Radiant Historia which you have already played a huge chunk of.I have no experience with DQ games prior to 9 (which is my current most played handheld rpg at 125hrs) so I can't recommend that.