How can I creatively reason to a player an imposed speed limit of his or her spaceship, given that in reality with constant acceleration a spaceship is only limited by the speed of light? I chose to limit the maximum velocity of a vessel, as it otherwise becomes (technically) impractical to engage with other spaceship in a (dogfight) combat.
If you're sure you want to limit the player to always having to do dogfight(I for one am an explorer type, so I'd just accelerate away every time), then you could for example limit the fuel in following way: The spaceships generate their fuel while not using their engines. This could be rationalized with a system of them bringing the components on board, but having to do some catalyst-process in order for them to create the actual compounds used as fuel. You can therefore only speed up for a limited amount of time before you require to "refuel".
How can I determine the ideal size of an average planetary system, the number of planets
I'd go for as random as they can get. Maybe a young star only has a huge asteroid belt and no planets, while some stars can sport a dozen or so planetoids and moons to boot. There's no way to determine "realism" for the average planetary system, as we don't have the technology to really determine other star systems currently. But for the explorer, vastly differing systems would increase the interest.
the time it could take on average to get a planet in the outer orbit to a planet closer to the sun, both in game time and real time? Ideally I would like the game to feel realistic and exciting to get across the planetary system, yet not feel too boring with longer periods of nothing happening.
This is going to have to be either/ or, but not both. If you go for any sliver of realism, then it's going to be boring for the action players. As an example, Elite Dangerous. Even with the automatic docking and star drives, the game still suffers from boredom of the huge distances, if you don't like the serenity of cruising around in empty space. The universe is huge and on average, empty. 697
Take the known planets to have life divided by the planets that don't have life and we'll approach zero quite fast. The distances are at best only mind bogling, and this translates to hours of boredom, even with your accelerated time frame. Kerbal Space Program also provides a good idea on how boring it really can get with any amount of realism: KSP has the whole solar system with its furthest away planet closer to the Kerbol sun than the Earth is to Sol, and still it takes several hours to transit even to the closest moon. Granted, the craziest missions where they just basically go with solid rocket boosters to the Mun and back take but minutes, but that's besides the point. Don't worry on the realism, create a balance of fun and "that's just ridiculous".
In a 2D game, the only realism to be had might be to pre-plan your escape from and entry to any solar system, using planetary masses to do a gravity assisted boost. But it only makes sense if the fuel for long distance traveling is scarce enough to justify not just simply turning the accelerator to 11 and aiming for your target.
However, if people can simply see the prevailing prices on each planet beforehand, there is not much challenge for finding the optimal trade. I can cut the communication but then how can I reason to a player that they can only see the prevailing prices of goods when they visit a planet, however, not when flying in space? Is there any other way to make trade more challenging and reason it to the player?
You can make the tonnage affect the acceleration, therefore slowing them down and making it risky to try and haul a huge mass of cargo across the stars for a profit.
The communication can be limited to either the nearest star systems. This can easily be justified with "signals can't go faster than light". This way you could have a system in play that shows a spreadsheet for the player on the known prices, coupled with the "age" of that information. These prices could even be updated on the fly, so as your flying closer to a star system, onboard computers update the price from signals coming from that planet(4 weeks old, 2 weeks old, week old, current).
You could only show the player prices from their last visit to any known system, and a list of planets with a shortage on some cargo. Combine this with the previous signal limitation idea, and long hauls would almost always be a gamble in terms of profit. 697