Well, my (late) opinion is that you play the pokemons you like, as simply as that, wether they are everyone favorite or not. I love Infernape over all mons and in particular over that weird chicken Blaziken, and I will NEVER replace the monkey although i understand blaziken is better. But same way if you really like a pokemon, keep it even if everyyyyyone has it. I had a Gardevoir in my main 6 before i started to come to the forum and even if I dislike the lack of originality, at the end what matters is the pleasure you have when you play.
With this idea in mind, i support your choice to put Dragonite in the box for now. For my second run of reborn (first one was a clasic and legit one) I reverted back to E12 to have a early game Gyarardos, and that was boring, this thing just swept alone almost all gym leaders so i quit this run. The game is very very well thought in term of dificulty and i think playing it how it was planned to be is how you get most fun of it