It's been a while since I stayed in Kochi, but here are a few places worth going to if you're in Kochi.
Paragon - This restaurant will feature in almost every answer to this question. Paragon has a very 'family restaurant' vibe to it, something that's rarely seen in new restaurants nowadays. The staff is very courteous, the food is amazing (Non-Resident Keralites, this is what you've been waiting for all your life!) and the food is priced economically (not too cheap, nor too expensive). The portions might disappoint you at times, but overall, a great place to eat to hearts content!
Kayees (Mattancherry) - Another regular feature in the list of Kochi's best, this little 'hotel' is everything you'd expect a great restaurant to NOT BE. Nestled in a quiet corner of Mattancherry, Kochiites swear by Kayees Ikka's biriyani. Prompt service, healthy portions and a lipsmacking biriyani. A must visit for everyone travelling to Kochi.
Mubarak - This blink and you miss restaurant right next to the Mathrubhumi Junction in Kaloor is a local favorite. You're greeted by the view of atlest 6-10 varities of non-vegetarian curries as you enter the restaurant and boy, they taste better than they look. The porrottas as always hot and fresh, even their appams and pattiris are better than most places in the city. My personal favorite is their Chilly Beef Dry Fry. Their biriyani is decent too, but my favorite would be the Porrotta, Beef Roast/Fry combo.
Cocoa Tree - A favorite among the kids growing up in the late 2000s. Cocoa Tree is your ideal place to chill with your people (if your plans don't include drinking i.e.).
Burger Junction - I've heard Burger Junction is a new fan favorite in Kochi and you can see people flocking to their outlets to have their fill. Probably the only state in India where you can have beef without fearing for your life and their beef burgers will make you realise how unlucky the rest of the country is. Great burgers at Great Prices, what more do you need?
I'll update the rest in sometime.