in BM-Merchant ship, you want to prioritize MS>Gold a good bit
I had a very hard time believing that this is good advice. It sounds like it is just your gut feeling - or did you do any simulations to back it up? It didn't sound like it, so I did them myself (see the second half of the posting below).
I don't think I would ever buy a Merchant Ship with $6 in a BMish deck - maybe unless I virtually don't have any terminal action yet. Regarding the latter, I am uncertain if I should buy a Gold or a Merchant Ship with my first $6 if I don't have any action yet. If I had to decide without simulations, I'd go for the Gold even then (because I may well get the $5 for my Merchant Ship soon afterwards with which I can't buy a Gold).
For the sake of completeness I'll shortly spell out the disadvantages and advantages Merchant Ship has compared to Gold, although of course Wandering Winder already mentioned the main disadvantage and the main advantage and #2 of the disadvantages is also really well-known - but #3 of the disadvantages may be a little less known:
1. Merchant Ship needs a terminal action. Having two Merchant Ships in your hand compared to Merchant Ship and Gold obviously makes a huge ($3) difference.
2. Duration cards can get caught in the reshuffle.
3. Even independently of #2, it is usually better to have $3 now compared to $2 this turn and $1 next turn. There are two reasons for this - the first is relevant until the end game and the second in the end game: First, if there is a reshuffle between the turns, then with $3 compared to $2, you would have been able to buy a better card getting shuffled into the deck. Economically speaking, this is a classic impact of interest. You'd rather have an extra dollar now and already get interest for it until next period. Second, the game might end before the bonus on the next turn so that you never get it.
Merchant Ship has the following advantage over Gold:
1. It nets you $4 instead of $3 when you have the action to play it.
I had a very hard time believing that this can usually make up the three disadvantages of Merchant Ship compared to Gold in BM decks.
So to see who is right I did some simulations with Geronimoo's simulator myself and they confirmed my gut feeling over your's...
I started with taking Geronimoo's Single Card-Merchant Ship bot.
I improved it by first moving up the buy rule for one Merchant Ship above "buy Duchy if Provinces <=6" and second adding another buy rule under it to prefer Merchant Ships over Silver (as long as there are 7 or 8 Provinces left).
I totally agree with you that in the early and middle game, you should prefer Merchant Ship over Silver. The benefit over Silver (netting $4 instead of $2) should be big enough to justify the three disadvantages mentioned above.
The simulations confirm this - my improved bot beats Geronimoo's standard bot (which never buys more than one Merchant Ship) with 53% against 37%. (It doesn't really matter if you set the lower "Buy Merchant Ship rule" to <3, <4, <5 or delete the limit alltogether - the result is always 53% against 37% from <3 on. The second one is the one that makes by far the biggest difference, "<2" still yields 52% against 38%.)
When we compare this improved Merchant Ship bot with a version where we let it buy the first Merchant Ship over Gold, it is equally strong - both of the two have a 45% chance of winning against each other - this sort of confirms my gut feeling that I didn't know which of these to prefer...
But when you start letting it buy more than one Merchant Ship over Gold, things get worse rapidly:
44% against 46% when letting it buy two Merchants Ships over Gold
39% against 51% when letting it buy three Merchants Ships over Gold
33% against 58% when letting it buy four Merchants Ships over Gold
The conclusion seems to be that it is not good advice to buy Merchant Ships over Gold in BMish games if you already have any terminal actions.