It's just the way that the defense section of the game is implemented. Build a bunch of the best research-able defenses to get any benefit. Build any of the earlier defenses, or not enough higher defenses and you get nothing.
On a slightly different angle from different UFOs attacking bases option, what if early base attacks were conducted by small and very fast UFOs? Early attacks could be one or two and carry a small party. As the game progresses they progress into larger groups of larger UFOs. Having the invading party split into multiple UFOs would also implement a way for defenses to reduce incoming assault parties. Say 3 UFOs attack, each carrying 6 aliens and you shoot down one. 12 aliens land. This way, early defenses like missiles could actually make a difference.
This could be balanced by the higher defenses having higher build and maintenance costs. Frugal players who don't mind occassional defense missions could choose to have a laser defense that costs far less than a fusion defense and lightens the attacks, which could save him the money he may lose in casualties from a full attack. Players who do not want base assaults could pay up for full fusion defenses. Players in the beginning of the game could build a missile defense and actually feel rewarded for his actions if a small UFO attacks early. I think it could open up the base defense side of the game quite a bit, as well as base logistics.
This should obviously be an optional mod, but I do think it would be a fantastic one. If the variables necessary to make it happen were available to edit, I would gladly make it. Namely which UFOs do which missions.