My husband is allergic to onions and peppers as well (I on the other hand LOVE onions) and he often uses a lot of garlic, cumin, ginger, mustard powder, and oregano to replace a lot of the punch that the peppers give, especially along with the veggies the other replies mentioned should work just fine. We have been thinking of playing with using dikon (a huge Japanese white radish) combined with fresh garlic in cooked dishes to replace the bulk of onions, especially when sauteed. I've cooked regular red radishes in a root stew before and they held together nicely.
Some of how you can make substitutions depends on your personal preference for spices & seasonings. Just think about the flavors that you like the best and decide on your own spice mixes based on how they would be used and how strong you like them. For example, if a recipe gets a lot of bulk/flavor/spice from sauteed peppers, you could have your spice mix for 'strong spicy' (cumin, ginger & mustard powder maybe) and add it to quartered sauteed crimini (baby portabello) mushrooms.
It has been a long road for me to figure out how to adapt onion and pepper heavy recipes for my husband, but it really comes down to finding out what your preferred close equivalent (in bulk and flavor) are.
Hope this helps!