Probably not a popular idea and probably too early in your dev testing cycle but...

Starting from scratch, killing 2 bots for 80 bounty and trading up from then on took only a matter of hours to amass north of 100K cash. After that losing a full cargo of 700 cost widgets and a special ship (thanks Phoenix) was an inconvenience.

This puts all the high end ships and equipment at one's disposal incredibly quickly for an online game where, presumably, you want people to play for months.

It condenses an ongoing sense of accomplishment into minutes and hours instead of days and weeks. Either profit has to come down or costs go up by an order of magnitude (or more).

There should probably be a cost of equipping and unequipping weapons, engines, batteries, etc as well. Paying the station crew either a flat fee or a percentage of the equipment being added or removed from the ship. Perhaps maintenance of ships, battery conditioning and engine overhauls, etc as well.

Also the free ships should not be free. They should send you into debt. Why repair a freebie when you can select a new one continually? They should cost at least a full repair value. Allow negative cash values and prevent purchase of anything without positive balance except the newbie bus (and possibly docking fees, maintenance and repairs).

Climbing out of debt and getting into cash positive would feel like you were making progress. Buying your first piece of equipment would be great.

Yeah, but if you got put into debt, a person would rather start a new character than try to dig their way out of debt. Since we've only had a wide variety of ships for a few days though, I think it's safe to bet that eventually they would make it tougher to get the more advanced ships.
Keep in mind though, that there is no real "best" ship. It all depends on your style of playing. I personally like the Centurion (considered the worst ship by some) because it's fast and agile. Others like the Prometheus because it can take a lot of hits. However, a good Centurion pilot can take advantage of a Prometheus's slow turn rate and take them out. All of the weapons are balanced, as well. There is no ultimate weapon (anymore). Just about every weapon type gets put to use by one player or another.

Well, I think that once more features are implemented, a player's goal will be more along the lines of trying to make their nation more powerful and going up in the chain of command than just trying to get the next more powerful ship. I find that games where all you do is perform a bunch of repetitive tasks (killing bots/monsters, running trade routes, etc) for no purpose other than to upgrade your character in order to perform MORE repetitive tasks get boring really fast. On the other hand, who wouldn't want to rise in rank and command a fleet of fighters or maybe even a battleship against the enemy's forces?

Or, if you're a trader, you can build yourself a good reputation by quickly and reliably carrying expensive cargo through dangerous routes, which will make the higher-ups in the various nations more likely to hire you for the more high-risk transport jobs. Or you could make yourself known as a badass pirate mofo that's not to be messed with, wanted in 20 sectors but never caught, the most infamous outlaw in the galaxy...

You make very good points, Savane, and I have mixed feelings about this sort of thing. On the one hand I agree that you need a sense of accomplishment to stretch out over weeks or months or years, but on the other hand if accomplishing things are too difficult many new players will become discouraged and will leave.

The biggest ship we have is 19m in lenght. I'd like to think that this is still down on the small end of what is possible. Basically, I'd want the design to provide servicable ships which could contribute to the game and with skill protect you from anything in the game but another skillful player, but which had rewards that were less easy to acquire. I think that is what the devs were thinking when they introduced the 'advanced' class of ships, which is a good start but (as I suspect they know) doesn't go as far as it needs to.

Much as I'd like to make extensive analysis of this, I think it is going to have to wait until we see what the devs have in mind for the mission structure.

I agree that the free ship should cost something for the reason you mention and for others, but at present the money structure is not set up to handle depts. I also think that dying should cost something, but we aren't ready to go there yet.

I'm not entirely sure I agree that tinkering with your ship should cost something. I would like to think that we could address that question after the introduction of a skill tree (ei 'mechanic' skill).

Yeah, not too worried about it yet as we are obviously very early in the development of the full game. Just throwing those 2c out there.

It is important though for players to realize that unpopular changes are a part of making a game more playable and enjoyable in the long run. I thought it was pretty funny after such a significant release as 3.2.0 that there was complaining about unbalanced features when we were specifically told it was unbalanced.

The closer to real game ready we get, the more howls of anguish that will come. But then we get to say "back in the day..." to the noobies.