Push come to shove, when you decide on running a ship based campaign you fundamentally have to decide how much of the business side of shipping do you want to deal with. I would not be surprised if most groups treat the ship economics with about as much attention as a TV show typically gives it.. aka "the ship mysteriously breaks even and all our profits come from the adventures". Because keeping a ship in the black is a lot of work. Unless you've got a ship with no mortgage, in which case it's a massive money spinner if the rules are taken literally. (which they aren't intended to be, btw).
I think that one of the larger small craft that's got quarters for the PCs (so you can take longer trips) and enough thrust to travel around solar systems is a great option. And I would tend to think that some kind of jump ferries would actually be pretty common to make hauling shuttles and system ships around reasonable, assuming you aren't just going to do an Expanse/Firefly style single system campaign. But it is one of the few play options that's basically doesn't have any published examples of in any edition of Traveller that I am aware of.
I think the ship shares the way Mongoose does them is not good. A few million credits is not enough to make a dent in a full starship and if you aren't doing a ship campaign it's kind of wtf now?. IIRC, T5 ship shares are basically just "you own 50 tons of ship", which you can claim now or later. So like 2 ship shares is needed to have a Type S Scout, while 8 is needed to have a Close Escort. I'm not sure just how frequently ship shares actually turn up (though Merchants seem to get a lot) because I've never put the T5 chargen through its paces, but that seems like a lot.
As I mentioned earlier, I like the T:NE method where ship shares are pooled and the players can choose what kind of ship category they want to go for and make decisions to put their shares towards bigger ship or newer ship or more paid off ship, etc. And, if like many of my campaigns, the players don't want to deal with a ship at all, there is a clear cash value (Cr10k) for unused ship shares. That leaves it in the players' hands. If they want to do star mercs or pirates, roll for a warship. If they want to be rogue traders, try the merchant table. Just want transport, there's the a table for that. etc.
I think that if you are going to have a ship, the ship should be a character in its own right and you should make it matter beyond just being how the PCs get from point A to point B. Because just doing without the ship is a lot less hassle if it's just an excuse to change planets.