I would definitely recommend the DS Castlevania Trilogy. (Dawn of Sorrow, Portrait of Ruin, Order of Ecclesia)

Pokémon X/Y are by far the best games in the series so far, but they probably haven't evolved in the way you're asking for. Pokémon Mystery Dungeon might appeal more to you.

Etrian Odyssey is a great take on making a truly old school RPG, and by old school, I mean *old* school. It's incredibly difficult, but very special. The first game in the series recently received a 3DS remake.

If you're going to play Phoenix Wright or Professor Layton, do them in order if you can (starting with the DS games). This is especially true for Layton, IMO. With Phoenix Wright, you may want to wait a month or two; they're doing a 3DS re-release of the first three games in Japan soon (April), and there might still be a US/EU release in the near future.

I'm sorry you didn't like Ocarina, it's still my favourite game of all time, bar none.

On 3DS I'd recommend:
Fire Emblem: Awakening
Monster Hunter 3 Ultimate (though I'd suggest waiting for 4 Ultimate)
Kingdom Hearts: Dream Drop Distance

For regular DS:
Contra 4
Castlevania: Dawn of Sorrow/Portrait of Ruin/Order of Ecclesia
Okamiden
Solatorobo
Chrono Trigger (If you haven't already played it)
Shantae: Risky's Revenge (DSi Download)

Actually, I fell it's a bit of a toss up. X/Y are definitely the best games mechanically, but the story (at least for me) was rather by the numbers. Pokémon Black and White had, in my opinion, the best story in the series thus far, bringing up some rather deep philosophic messages/ideas for a kids game. It's a personal preference thing, I just wanted to toss in my two cents.

Sweet! I hadn't heard about this. Hopefully this will sell well enough to convince Capcom to finally release Investigations 2 outside Japan.

DS/3DS Ace attorney series!

I would definitely recommend Fire Emblem Awakening and the Etrian Odyssey(I'd say start with Untold or IV, no need to play them in order) games. There's a lot more I'll post a better list when I have more time to post.

If you enjoy Bravely Default then you'll enjoy Fire Emblem.
Professor Layton series: beautiful puzzle games!!!
Shin Megami Tensei IV: if you like jrpg then this is another must.

It was rather easy to guess who the bad guy was. It was like they placed a sign saying, hey everyone this fucking idiot right here is the freaking bad guy! Stop them!

Pokemon x and y did cut down greatly on the grinding and like black 2 had barely any need for hms outside of surf and fly if you wanted to travel inbetween the towns quickly.