I think the fact that you can no longer up the IL-2 for base deffence when the fighter hangers are down may have been another factor in it's declining usage. I've seen a swarm of them stop what should have been a clean base capture several times. Would have liked to have seen how well they fared in this role without F3.
This +100
I tried to take an IL-2 up in base defense where the FHs were down, and couldn't. It surprised and disappointed me. Base defense when FHs were down was probably half or more of my sorties in it. Now that it isn't an option (which is completely ridiculous, it is a bomber, i.e. an airplane designed to hit ground targets, and not a fighter, i.e. an airplane designed for air superiority), I won't have the same reasons/opportunities to fly it.
None of the remaining bombers are very suitable for base defense under horde conditions. Most simply don't have sufficient hitting power to start evening the odds, and the ones that kind of do like the A-20 or B-25, are even larger and more lumbering at low speeds than the brick IL-2.