To make vegan: I haven't tried it but I think you can replace 1 egg with 1 flax egg.
Honey: You can substitute honey with maple syrup.
Flour: You can replace whole wheat flour with white flour but your muffins might be a little more dense. I would not recommend almond flour, coconut flour, or oat flour. You can not substitute these flours 1:1 with whole wheat flour.
Nuts: You can add pecans or walnuts
Mini Muffins: You can make these into mini muffins by cutting the bake time in half.