Toonol, you are right that sometimes a stacking of Advantages onto a Power can get ridiculous, so your approach could be considered valid in such a case. OTOH, there are cases when the cost of subsequent Advantages is factored into the size of an Advantage.
Let's take Armor Piercing for example. A 15 Damage Class attack is the same Active Points as a 10 DC attack with Armor Piercing. AP can be neutralized by Hardening the appropriate Defense, which would probably cost less to the defender than buying enough Defense to blunt the base 15 DC attack. But any subsequent Advantages added to the AP attack will be less expensive than if they were added to the higher Base Point Power, which balances out their utility.
Changing the way Advantages are calculated would be most appropriate on a case-by-case basis, which would probably be more work than it's worth for most people. It's more efficient in the long run to keep one standardized method and allow the GM to rule on what is or isn't abusive as it comes up.
FWIW, what you're describing was the way in which Reduced END Cost was calculated before the 4th Edition of the HERO System: you added up the cost of all the other Advantages, then applied the RE Cost modifier to that total. Obviously, that approach didn't last.
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-- RexMundi
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