Hm, I'm thinking that without upgrades, particularly for units, there arent enough ways to have much influence on battles already started. In my own strategies, I use unit upgrades to sorta give things a push when needed; as with many things in the game it might help, it might not.... but it's a very useful tool.
The problem is.... alot of the time, it's the *only* viable tool. Everything else is expensive or very risky, or both. Pretty much the least risky/pricey thing after that is dropping mythological things in there to shove the balance of battles around. EDIT: This is most true in the early game, or if I've already been using a number of bigger effects (and thus it's a bad idea to throw any more out), yet I might have to affect combat happening away from that stuff, or something like that.
Building upgrades I originally thought useless, but witht he changes to the ways cities work, I find myself using them to protect key buildings from bandits and such so they dont get locked up for 10 turns, screwing things over. As best I can tell, building upgrades just improve the max health of the building, yes? This actually seems almost necessary in some cases; there are some units that can just clobber a building in a single monstrous blow (WITHOUT being a Trojan Horse), and I've had a few cases where I probably WOULD have been in trouble if I hadnt been able to use that to at least slow the rampaging enemy unit down so I could get guys in there to deal with it.
But yeah, that's my main problem, not enough low-level ways to influence things that are already out. Buildings only help with FUTURE units, and that means it can be many turns before they really do something, and by then, the situation may have changed for the worse, to where now the building is hurting more than helping. AKA, I find them to be useful tools, and I think they might be MORE useful and versatile once the cataclysm system is in.
Without those, all that's left is Smite (which really is a good tool), and Commandment (which is currently bloody useless, that might change with cataclysms but I still think it'll be a rare-use item)