"I think it would be better if the upgrades in the tree were more expensive but independently priced"
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I have been thinking of some kind of game, where EVERY upgrade starts at maybe 1 cost, BUT each time you buy something, that item becomes more expensive (+1?) in the next run, so over multiple runs the pricing sorts itself out (NOW, apply this to a networked game & compare EVERYONE purchases).
There also NEEDS some form of "price decay" too, or EVERYTHING will become too expensive. Maybe at some kind of "prestige"(?) everything becomes -1 cost, so the most bought things are still expensive, but the less bought things becomes cheaper.
Now, imagine what happens when this system is networked to ALL players, because people have different play-styles, they might keep the prices low for other play-styles.
What this system fails to model, (for networked: is the individual play-styles, maybe a good thing?) is the change in a players priories from low level to high level.
One way to model this could be either a price increase or decrease (not sure which) the more you have progressed.
Another problem with this system, is that at its worst implementation, it would eventually force players to play with only their least favorite (trash) builds, just to "grind down" the cost of the actually fun upgrades (it's NOT what I want).
At its BEST implementation, it would fairly price each upgrade, AND encourage (without forcing) the player to experiment with new build combinations, because the best upgrades are a BIT expensive (not ridiculously expensive).