I agree. I've tried both ways...and one at a time (if you have the time, like on the weekend, instead of work days), makes it feel like you're more involved in the game.
I'm working on my Metal and Air shrines right now, and am working on feeding Chromes to level 15 one at a time. Looking back, I can see where I made a lot of mistakes in strategies. Just by rushing myself too much. Sometimes I leave a treat farm open just to buy peppers one batch at a time, or mix up breeding times with Chromes, Mags, and mixing in some Airs or Sandies.
Working on getting 29 Pans to level 16 put me over the edge. ;0)
Have Fun!
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Are you going to try to get all your Pans to 20? That would look amazing. . .