I have a floor of 1kb when calculating the fee per kb.
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... if there's a good practical argument on the spender's side, then I would change it. #1 is utility for users.
An argument for your consideration -
1. The purpose of the graph is to help users decide what fee rate to pay with their transaction.
2. The assumption is that miners (mostly) prioritize transactions by their fee rate, so by looking at the intersection of the graph with the line y = <typical max block size of 750-1000 kB>, we can gauge what fee rate is required to get into the next block, if it arrives now.
3. Miners do not, however, use a floor tx size of 1 kB when calculating fee rate (not in the reference implementation i.e. CreateNewBlock, nor is it economically rational - a miner should prioritize for example a 250 byte transaction over a 1000 byte one, if they are both paying the same fixed fee).
4. Therefore the data as presented now, with the floor size, is distorted with respect to its purpose in (1).
As a concrete example, consider a flood of 250 byte transactions, each paying a 0.1 mBTC fee. On the graph, it will show up as a fee rate of 0.1 mBTC / kB, because of the floor.
Next, consider a user who wants to jump ahead of the queue, so he views the graph and says, OK, I'll pay 0.2 mBTC per kB instead. His transaction is say 1 kB, so he pays a 0.2 mBTC fee.
However, in reality he would not have jumped ahead of the queue at all, because the fee rate of the flooded transactions (0.4 mBTC per 1000 bytes) is higher than that of his transaction. So, he was not helped by the graph.