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If I'm playing the game through, I'm using the one where it displays the party. If I'm chaining, obviously ap 20. If I'm doing anything else, I like the rustic clock...
I would use the daycare like the rest of the nubs here, but I have yet to beat this game yet so I'm not focusing on breeding or getting EV/IV shiny rofl hax pokemon yet.
The friend app and Daycare checker are my most used Apps (Not counting the watch).
The first one is useful for whenever you get a Pokemon like Happiny while the second makes it less of a hassle to level up your Pokemons through the daycare.
I have a hard time beating the game without them!
Definitely the step checker and day care apps. I check with the day care app to see when I have a new egg, and then reset my step counter and eagerly await my new pokes.
I use the chaining app and daycare app the most. I have recently spent a lot of time breeding to get some good moved Pokemon. I use the step counter quite a lot as well.
It's between the breeder, chainer, berry apps. It all depends on what I'm doing at that point and time really. Like yesterday I was breeding alot so I had that app up and then later I did some chaining. So really just a mix of those three.