For the cake - replaced about half the vanilla extract with lemon extract (would have done it all but I ran out); replaced about 100mL (a little less than half) the water with lemon juice. Was delicious with the lemon glaze on top! Did not make the berry compote this time.
I used 2 cans of white beans instead of pasta (which the original recipe called for), and omitted the nutritional yeast. I also used very little oil. I thought this was a good, filling meal and will make it again. Next time use a larger dish so the tomatoes cook a little more evenly. I've updated my recipe to reflect these changes for the future.
I used self-rising all-purpose flour, added some almond extract along with vanilla, and ground up a flax/chia/hemp seed blend in place of flax seeds. Also added a small amount of chopped pecans and vegan semisweet chocolate chips. It cooked for about an hour to get to 190*F internal temp. Tasted delicious fresh from the oven!
Used maple syrup instead of honey and frozen broccoli instead of fresh. Prepared sauce the day before. Eliminated most of the neutral oil (a few sprays of oil in the pan at the beginning is all). Liked it a lot. Will make again!
Updated recipe with my notes. Made 12 servings (1.5 of original recipe). Good basic muffin. Could go less on the sugar if you want it to be less sweet.