Kaede is a good fave to have.. I don't think I'd be able to pick a singular favorite character for the entire series.. ( ◡̀_◡́)ᕤ

I think for me, it goes:
THH: Makoto&Kyoko. They're a package deal. Alternatively, Fukawa-chan. The entire cast for the first game is just so good though.. THH is my favorite game out of the three mainline ones which you wouldn't guess if you see how much I talk about the OTHER two hehehe..
SDR2: The main trio (Chiaki, Nagito & Hajime) are too easy of a choice, so I'm going to say... Fuyuhiko? I really, really love Pekoyama, but I like her more in a "I see myself in you" way than anything else - I find his reaction to [SPOILERS] and the growth it forces him to have as a person so sweet.. I think about him 'introducing' himself to everyone more than I ought to.
NDRV3: I love Amami-kun... I wish we had spent more time with him (ᵕ—ᴗ—). His events in Dangan Salmon Team are really interesting and I think he's really funny. V3 is a game I have a hard time meeting halfway because I simply think its ideas and execution both are kind of.. mehh. But I can't really think of a character I actively DISlike.. which.. in some ways is kind of worse? At worst, they're forgettable. If I were to pick runner-up faves.. hmm, I also like Harukawa in a "I see myself in you" way, and of course that means I like Momota-kun and Saihara-chan as well.. An unpopular favorite I have is Shinguuji, I guess? He made 13-year old Dessie want to get into anthropology really bad, ahaha.