I've been playing a lot of games for my 3DS. Right now I'm playing through Fire Emblem: Awakening and enjoying it a ton.
The older I get the more I move away from real time strategy games and start to appreciate the turn-based format. It's not that my reflexes are bad, I'm only 26, but I just don't have time to devote to getting really good at execution in games. I'm usually playing less than an hour each night and I'm lucky if that is one uninterrupted block of time.
For me, right now, Fire Emblem: Awakening is perfect. It's a turn based strategy with interesting mechanics that I can suspend at any time. I constantly have it near me since my 3DS is almost always close by. It's great to be able to take a turn and then put it down to come back to later. Even if I know I only have 5 minutes I still get to make some progress and stretch my mind with some strategy.
It's more character driven than most turn-based RPGs I've played. If you're a fan of character growth and interaction it will be right up your alley. Some great character development and customization ties the whole game together.
I've recommended it to everyone that I know who owns a 3DS. If you have one you should definitely look into it.