Not much off the top of my head to be honest.
Any change to the timing either will make flares useless (an extra 10-15 seconds makes it too easy to disarm, less time makes it too hard), reducing damage to buildings sort of negates the point (Why try to sneak in and use this if it doesn't kill anything and gives the enemy a bunch of points if they disarm it?).
Then again, maybe they could have damage reduced on buildings, but increased on units. So instead of just, oh hey there goes our barracks and War Factory because of a flare, GG, the A-bomb essentially obliterates infantry and vehicles in the entire base, leaving a brief period where the enemy would be very open to an assault. I know this has been the opposite of what patches have done (I believe some vehicle armour has been made more resistant to A-bombs?), but rather than this 1-hit GG, it could make flares into a really good support weapon.
It would also discourage the 'lone wolf' style with flares. Where you just buy your Jeep and Tanya and head off on your own, instead you'd have to coordinate with your team to launch an assault.
This might also be a lot of work though, considering building cover and terrain types affect how much the bomb damages I believe? Also when anything isn't OP offensive in this game is tends not to get used as much (See the history of medics).
Not trying to hijack the thread with this at all. But tweaks to the flare system may also discourage a lot of roof camping.