Having played over 7 hours so far I'm having a great time, and enjoy every minute of the game. However there are some issues I hope could be changed in later builds in order to make the experience even better!
So, without further ado:
-showing how many sovoereigns we have when shopping (i know i can see it by opening another tab, but it would be nice not to have to do so)
-enabling player to highlight encountered enemy, to see it's health bar or at least the name of what I'm fighting
-lowering the cost of using bat (seriously, it's so expensive I rarely use it)
-increasing cargo hold of your first ship/train (in Sunless Sea starting ship had 40 units, now I have only 10, most of it filled with fuel and supplies)
-lowering the price of things to buy in shops/increasing income for completing quests (at least in early builds)
-enabling player to buy new ships, preferably for lower price, to help us see what to look forward to
-allowing us to fly not only over or beside floating rocks, but also under them (some kind of animation i suppose, to increase the feeling of being in space)
-adding more enemies/random encounters (so far I've only ever fought with Tackety Scouts or flying pink fish-things)
-perhaps adding an option to change difficulty or how often random encounters occur
-some minor bug fixes, adding a pause option and hotkeys for those icons on the bottom of the screen

And that's all for now. As I've said, im having so much fun playing Skies and already feel it'll be a great game. Also, what made you think of making a train into a spaceship? I get that ships are a no-go, and zeppelins are hard to differentiate, but still, I wouldn't think of a train in the first place.

Best Regards