my 50 cents

1)planet costs: it's a little bit strange that the amount of fuel you need to get to a planet isn't depend on where in the system you are. Of course making that 'more realistic' would almost require a change in which the planets are not in a row but on elipses around the sun and i understand if you ruled that out. On the other hand if you don't care for realistic distances that might still look quite neat. If you really want to push it, you make the location of the planets around the sun time dependent. That means when you come back to the system the locations of planets and therefore their distances (and prices) to each other are different. Once you start with having a small sun icon in the middle and having planet icons around it, you can go crazy and have systems with two suns, or a sun rotating a black hole.
2)ship dependent technology: until now basically the only factor how to chosse a ship is storrage size. Even the ship that contains of a cross can almost host all technologies because very few technologies have more than two addons. So once you're on the tree ship, your not going back. That would change if not all technologies would be compatible with all ships.
3)merging elements after mining: drag-n-dropping 5-He over a 4-He in storage merges it to 9-He. That doesn't work if the 4-He is not on the ship, but in the mining-bar. That rarly happens but it feels strange, when it does.
4) drag-n-dropping an element from storage to space should open the drop-dialog.