I think the upgrade cost card is a good one, what the system is designed for, precisely because it's one you'd never run for long periods of time - it rewards planning and timing and micromanaging (some might say it necessitates it, which could be annoyingly fiddly to some people, but the OP disproves this)
Biggest flaw with it I think is that it's too strong. It makes me almost never want to upgrade more than 1-2 units without having it in place. I mean, say you have 20 units and you're running the -1 gold per unit card. So basically that card is worth 20 gold per turn. But upgrading a single archer to a crossbow costs 200 gold. So the 50% upgrade is worth 100 gold. So even if you are upgrading just a single archer, you're better off to swap out even if your next civic is 5 turns away. And I'm usually upgrading more than 1 unit at a time. In fact, that's one of the rare cards where I'll actually sometimes even manually buy a civic change, since even if it costs you 100 gold to do the civic swap, if I'm upgrading 2 archers it pays for itself to do that for the one turn before I wait for my next civic.
tl;dr: 25% off upgrades would probably still be powerful enough that I'd use it.