good grief, you have to be playing like a pudding to lose cities once you have MI, even just fortified in a town they are defence 27! when you have a metropolis with a civil defence and nearby radar tower they are defence +225%=48.5!!! more than twice the attack of MA.
for heavens sake use armies filled with the best assault units you can get, they almost always will bust a defender in even the biggest cities. In the late game when you (hopefully) have a military academy and pentagon they are utterly amazing,, build the Military academy in your most productive city and then churn out armies there, pretty soon you can have several units with ADM 24,16,3 and 16 hit points. nothing stands in the way of that lot, you just have to make sure that they don't get caught on their own, keep lots of other MIs and MAs with them they are not a war machine on their own until you have at least a dozen.
You have to remember not to wait, for them to be useful you have to USE them. keep them empty until you go to war, THEN fill them with hte best unit available, if you fill them when you get them the units will be obsolete by the time you are ready for a war. remember though, you only need 1 to get the heroic epic, then the military academty, then you can build more to get the pentagon... I use my first leader to make an army, then use all the others to build wonders in 1 turn.