Preheat the oven to 400 degrees(F).
Put the cubed eggplant, grape tomatoes, onions, garlic and thyme on a large sheet pan.
Drizzle with the olive oil and a few pinches of salt and pepper. Toss to coat the veggies. Roast them for 40-45 minutes or until they are soft and starting to brown.
Remove from the oven, then turn the oven up to 450 degrees(F).
Let the veggies cool for a few minutes, then remove the thyme sprigs and add everything else to a food processor.
Then add the tomato paste, lemon juice, balsamic, agave or sugar, oregano, basil, red pepper and a pinch of salt to the food processor.
Pulse the food processor until the puree is smooth, but still has a little texture.
Now, press your pizza dough out evenly on to an oiled sheet pan, I just use the same sheet pan I roasted the veggies on. I put 1 1/2-2 pounds of dough, this will just depend on how thick you want your pizza.
Now, spread the pizza sauce out evenly on the dough. Then top that with the eggplant puree and spread that out. Top that with the vegan cheeses.
Bake for about 15 minutes or until the dough is brown and the cheese is as melted as it can get.
Remove from the oven, top with fresh basil and more red pepper if desired. Cut into to squares and serve!