I guess you are right about Pirate Ship being too weak (especially in 2P games) to matter as much, but even Miser has not only advantages over Signalman - so I'm not sure it's too weak. For instance, if you can't line up Signalman with a Copper, it doesn't just whiff. Also, compared to Signalman, you suffer not 1$, but 2$ loss the turn you use Miser to build up money. Signalman can be useful in decks with other strong trashers, whereas Miser is redundant with those. Also, the tokens can still be used as a defense and it costs ever-so-slightly less.
About Gladiator, it isn't always worth 3$, and Fortune isn't something you get by Gladiator, so counting it as something seperate from those free Golds leads to the wrong impression.
I don't recall Donald saying that he'd put Embargo itself on the piles, but you might have newer information than me. Last time I checked, he said that putting Embargo itself on the piles (as done in the beginning) was confusing to people, and so he changed it when it was clear there could be tokens. Similar about Pirate Ship confusing people when Treasures on the mat were worth more than 1$. Maybe you can link to where you got that information? I do recall him saying he'd have preferred Adventures' -Card and -Coin tokens as States, but that's another bag. One thing they have in common with Nocturne'state for example is that they are given to players at some point and can be removed later.
Also, I don't agree to Embargo being a dud. Our games have shown me that you are a much better player than me, so maybe Embargo is weak from an experienced player's perspective. But it shapes a game, as you can't go for certain strategies without being punished (ergo it's not pointless), and I also believe it is relatively popular. My favourite Seaside card togegher with Haven, actually.