DS
Shin Megami Tensei: Strange Journey. A hardcore first person dungeon crawler where you make contracts and recruit monsters to fight with you against other creatures. It has slight c&c and your alignment decides who you will fight in the end and your endings. It's Pokemon (only except SMT did it before Pokemon) mixed with Wizardry.
Hoshigami Remix. An extremely difficult srpg. It's similar to FFT in grid-based and class and level system, but how it works is that the character system is based on which god you choose to worship and their element alignment. There are also three other systems: RAP: Instead of the typical one moment-one attack on each turn, you can continue taking action (moving, battling, magic, whatever) until your ready-for-action-points gauge is filled. You can overfill it but it'll slow down your next turn; Coinfeigm: each coinfeigm had their own spells that can level up and customize (sort-of a derivative of FFVI's relics). Combination attack: is when you can have your character can "shoot" your opponent a step back next to your "session" character(s) can in turn attack the opponent again.
Infinite Space: a 3D RTS/space simmish game that lets you control a ship and emphasizes ship customization along with which characters to be with you. It also has c&c.
Dragon Quest V. It's Pokemon (DQ did it before Pokemon too) with a ton content and exploration. You can also choose which bride you want to be with.
Etrian Oddyssey III. It's also a hardcore first person dungeon crawler. In this version, there are 12 new classes with the ability to sub-class and ship voyages depends on your preparations. There is also three different endings depending on which city you side with or neither. You can upgrade your weapons through forging.
Chrono Trigger: A port of an SNES game that uses time travel as its gimmick. There are 13 different endings you can get based on changes you make. One of the most notable ones is that you can kill the main character and have a villain join your team. It's easy going and has more content than the original.
Puzzle Quest: Challenge of the Warlords: It's Bejeweled with experience points, story, and partners to bring along with you.
The Dark Spire: Another hardcore first person dungeon crawler. One of the few non-animuish jrpg. It's a throwback to Wizardry and your alignment decides who would battle with you and skill points. Three different endings too.
Pokemon Mystery Dungeon: Explorers of Sky. It's rogue-like dungeon crawler where you play as actual Pokemon. You get your main character based on gender and multiple choice questionnaire the game sets up at the beginning. You won't always get the same Pokemon for yourself but it can be a pain-in-the-ass if you're picky on your preference (I always try to get a Totodile or Treecko). Fortunately you can choose your partner who will always be a different element than your PC. You can recruit other Pokemon too.
Rune Factory 3: An arpg spin-off of the Harvest Moon franchise. You grow crops, fish, and woo people like HM but instead of using farm animals like the HM series, you battle and befriend monsters from dungeons to help you on your farm. The Rune Factory series tends to be samey like the Harvest Moon series so I recommend the third game since it has new dynamic schedules, interactions, and villagers can help you battle in dungeons.
Mario & Luigi: Bowser's Inside Story: It's not the most
game but it has a fun story that let's you play as Bowser. Its gameplay is turned based with mini-games as your attack. It's pretty short so if you don't feel like heavy rpging, choose that one. Warning, when you inhale as Bowser, hold down (or keep pressing, I don't remember) the y button along with repeating the x button. The game tells you all you need to do was button smash x to make Bowser inhale and it is lying.
3DS
Fire Emblem: Awakening: Best. Fire Emblem. Ever. In this game, you can customize and create your own character, class system with the ability to change like in Shadow Dragon, branching choices for units to promote in, Dual Strike with a supporting character, have children with the support character of the opposite sex and used the children in battle as well like in Genealogy of Holy-War.
Shin Megami Tensei Overclocked: A tactical rpg brimmed with c&c. Like FFT/FE/Tactics Ogre, you battle on grid-based with similar rule of attacking when you get next to the enemy (unless under certain conditions) with a turned based traditional SMT battle. You get monsters not through contracts necessarily but auctions.This version adds an eighth day and 2 more endings (4 in original).
Crimson Shroud: A tribute to table-top where your dice roll affects your battling. You move your character over a map. You don't level up, but you can use multiple die and fuse equipment.
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Again, my plans to cut down on vidia games have been foiled. 
