Tip 1 - In my opinion, you should flat out ignore the crew and power suggestions entirely. To determine if you need more crew, or power, simply pause, select everything using Ctrl A, Hit delete to delete everything, and then hit Ctrl Z to undo this delete. If done properly, the entire ship will now be reset to square one. Then you can simply time how long it takes for the crew to distribute power/ammunition throughout the ship/their module. This gives you a much better picture of your ship's "boot time" then the meters will ever be able to.
Tip 2 - When building a ship of any kind, always check for possible weak locations, especially against railguns. Always check each section of the ship to make sure that a railgun can't make it to a reactor, at least on the first hit.
Tip 3 - Always include more than one FE in a given module. If you end up with a fire that is too much for the crew to handle, opponents can simply flee, and let that section of the ship burn to death. Try to include 2-4 FE in regularly-sized modules if you can.
Tip 4 - Make sure to do at least something about missiles. Every ship needs point defense, and it is easy to underestimate how much you really need. Also take note that missiles often loop around and behind ships (unless they are a wall), so you will want point defense there too.
Tip 5 - When you are done creating a ship, make sure to test it against every other type of ship that you can think of. No matter what kind of ship you build, or how well you build it, it will always have a weakness, or counter of some sort. Figure out what your ship is weak to, then use that knowledge to pilot your ship in a such way that helps cover up your weakness.