Question 1: How close to Aurora are you aiming for? Will some things be implemented quite differently?
In the OP of the old
Pulsar 4X thread, the project is described as a "fan sequel" to Aurora. IMO, this sounds like you're mostly aiming to be a modern remake of Aurora. I'm surprised you're not calling this "Neo Aurora", "Aurora Redux" or similar. Having a different name may be a bit confusing if the game isn't all that different.
Question 2: For the things that are different from Aurora, will there be options in an Options or Campaign menu to turn them off/on or adjust them?
Myself, I don't believe there's such a thing as having too many configuration options. Leaving the most popular choices as default and allowing the rest of us to customize is what I'd prefer. And it helps avoid controversy over whether this feature or that should be added or left out.
Further: If you have any plans at all to allow others to create
mods for Pulsar or easily change it to suit their play style and preferences, I recommend that you design for this sooner rather than later.
I'm reminded of the development of Gnomoria. The developer had to rewrite a large portion of the game to accomidate modding and this took a lot of time. It used to get frequent, regular updates. Some were complaining about the sudden lack of updates and new features, though many were understanding and appreciative of the ability to create and use mods.
Instead of having important data (like the values of weapons and armor as well as pointers to graphics files) hard coded into the game, most of it now resides in easily edited text files in a database-style format. Also, it now has a means to install and uninstall mods without having to mess with the actual game files.
In a way, I'm also reminded of the development of Planet Explorers. About a year ago they decided to migrate the engine to Unity 5. This created tons of bugs and unforeseen consequences, forcing them to put story development and features on hold. Their time and resources were spent on the transition and fixing things. Over a year later and only now are they about caught up with their original plans.
Just saying that, for major changes like that, sooner is better than later.