Some incrementals simply have it so the prestige tree upgrade not only upgrades the item but resets the cost as well. So, if you have 5/10 levels on the talent tree, you'd start the run with 5 levels, but the initial cost is the same as if you were on the first level, and continues to scale accordingly.
Just an idea if you haven't considered it yet. There are other valid solutions to this problem, as you mentioned, of course.