Some of your suggestions are good. I will look more closely at the ships and their setup, though like I said, it wasn't always designed to generate uber-ships that can just wallop through the game. You always have to have something to upgrade, even on the purchased ships, otherwise the upgrade ships feature sort of loses its point.
People will just wait arounf 30-40 turns and then buy a monster ship and that's it. Some of the ship market ships do have special bonus features not available through purchasing on rare occasions (weapon bonuses, money bonuses, better gas mileage, slower durability wear, etc). Adding more different bonuses (there are about 45 of them in the game now) may be an interesting idea.
The mutual funds at this point were designed to be risky and nebulous, and weren't really designed to provide a lot of info as far as when to put money in (this game wasn't ever designed to be a paint-by-numbers, wait-until-the-indicator-says-its-ok type game). You have to follow the trends (and there are trends over a period of time) in your own mind and invest accordingly. Same with stocks (though the stock page does have a news report and a past 7 turns "ticker" to help you out mapping trends). Each stock definately has a "weight" in the game; some will go up and down very erratically, some will stay fairly steady, and some will slowly move up (or down) the whole game, more or less. It's up to you to figure things out. No big flashing signs here.
As far as the 10,000 shares rule, that was put in place to prevent people from sinking all their money into a low priced stock, then just waiting, and if it goes up enough, they just sell them and win the game. It's a game balance point to make the stock market a factor in a player's success, but not the ONLY factor.