I really like your reply, Spence. Here are my thoughts generally along the same lines.
I admit that I am one of the less lenient ones -- particularly in situations like the 5200 one where the "fix" is so easy... if a player could have simply verbalized the amount of the bet/raise and that statement would have prevented the 'irregularity' from occurring, and no one else (dealer/player) was at fault, I don't usually feel justified in making exceptions. By ruling strictly, there is less of a subjective element to decision making, less risk of being accused of favouritism, and doing so is more likely to result in more consistent rulings. The supposed 'intent' of the player is an important factor, but not always the defining one IMO, especially if the 'intent' is only made clear after some after-the-fact explanation by the player when the visual evidence of the wager contradicts the supposed true intention, and objectively the action at issue cannot be seen as a clear mistake. If the bettor's true intent were the only consideration, then we would not even have such well-established rules as the single oversized chip rule.
That being said, the situation in the original post is different from the 5200 case, in my opinion. We are not talking about a situation where the intent of the player is at odds with what the bet would visually indicate to players without any further explanation. The true intent of the player here is more likely a raise to 500 than something else contrived like asking for change, and the bet of 500 that remains in front of the player looks like a 500 bet to any observer. The fact that these are consistent should be given significant weight, and it makes sense to me to lean towards ruling this as 500 unless there is a rule that clearly would suggest the outcome should be different. Contrary to the people who voted the action as being a call (largely citing the oversized chip rule but not really thinking about the purpose of the rule), I don't think the single oversized chip rule being a call clearly covers this situation because there is no outstanding bet to be called. You have to force a creative interpretation of the BB "calling zero" to try to get the rule to apply. IMO, the spirit of the single oversized chip rule is not in play here. Therefore, it makes sense to me that the raise should be to 500, and I don't see why this wouldn't be a fair outcome.