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You'll notice that the net difference EV in the 20:2 vs 20:3 example is larger than the difference in the 10:2 vs 10:3 example.

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And herein lies your mistake. This simple pot odds expression does not denote your "value" in the pot. If the pot had 1000 bets, and you had to pay 1 or 2 bets with your flush draw, paying 1 is clearly not twice as valuable - both are extremely valuable for the option of making ~300 bets at the cost of 1 or 2. Comparing 1000:1 to 1000:2 for value is obviously incorrect.

The actual value of your hand is simply this:

EV = Pr(win) * (pot + bets won) - cost