Big fan of the DS and 3DS myself. Glad to hear you're enjoying Code of Princess, it's easily one of my favourite titles from last year. TWEWY is one of the DS's better and more unique titles, it's a good one to pick up next. It sounds like you've got alot to play for the next while, but i'd also like to add myself to the people who recommend 999 and Radiant Historia for the DS and Crimson Shroud on the eshop. Crimson Shroud is a Matsuno game and its presentation and gameplay is like a table top rpg. 999 is a really cool mystery/horror visual novel with puzzle elements. It has a sequel on the 3ds and vita called virtue's last reward that is more then worth your time. If you like mind blowing plot twist after plot twist and excellent characters(but can stand some long winded exposition) these two games need to be on your radar.
If you enjoyed the Contra series, Contra 4 is an awesome DS game. Check it out.
If you like some wackiness and rhythm games, Elite beat agents is pretty great. One of the more satisfying ds rhythm games, and with some great humour.
You mentioned Atlus games; maybe you might be interested in SMT Strange Journey and the Devil Survivor games on the DS - Devil survivor 1 has a 3ds remake called Devil Survivor Overclocked which adds content to the end of the game, fixes some balance issues and adds voice.
The trauma center series is another Atlus property. These games have you using the touch screen to open up patients and perform surgeries. It gets pretty over the top as you move from simple procedures like resetting bone fragments to cutting, sucking, zapping and tapping crazy super virus things. You end up having to problem solve really fast as you try to slow the spreading of cancers/viruses while keeping your patient alive. If you want a good challenge for your reflexes, then check these out. Mind you, the first ds game has a excellent wii remake that is followed up by two wii exclusives that add coop and new medical roles for the player to play. Still, they're good on the DS.