GPS/WAAS equipment cost is just a fraction of the total cost. What's expensive is the actual cost to retrofit each and every individual aircraft. It's not like you one simply unplug old equipment and swap in new ones.
You need a team of engineers a full week per aircraft at a minimum. If you stick to the OEM providers (Honeywell, etc), just the labor costs alone would be in the $ hundreds of thousands per aircraft. Then you have to add the cost of flight testing, cost to upgrade the simulators, cost to re-train all the pilots (and update all the training materials, manuals, job aids, etc), cost to train the mechanics, cost to provision spares, project management costs...
Plus it might not make sense to just upgrade to GPS. You'd probably package the upgrade to also add ADS-B, maybe CPDLC, even a HUD. Perhaps even more exhaustive upgrades are justified for older aircraft (older A320s still have CRTs).
Pretty soon you're easily past $1 million per aircraft...