Suggestions once more, sorry for any repeats...
The ability to name just about anything in-game. Solar systems, planets (as with SEIV), etc. etc.
The ability to classify enemy ships. Right now, with SE4, all the enemy ships appear in one long list. After contact, let us see the breakdown of classification as we see with our own ships. Let us be able to click on an enemy ship in the solar system view and have it pull up any info we have related to it (size, weapons, etc.)
Make this an option on set up, ships in an enemy fleet are not shown with a total number, but a guess of how many are in there (1-5, 6-10, 11-20, 21-40, etc.) This way fleets can have another tactical advantage- this might also allow for long range sensors to act as counter, thus increasing their value.
If possible, instead of trying to guess what all should be included in the text files, try to make it open ended so that the user can define what the lines do themselves. Not sure how to go about it, but perhaps there is a way that the user can define what "general restrictions/enable 1,2,3 etc" means.
Again, try to include user defined resources so we can change the pics of the exsisting resources and add more. Allow us to change the name of the resources so we can call it "money" or "industry" instead of organics or radioactives. It's just a label afterall, give it to us.
If at all possible, allow us to include more user defines resources- they don't have to be used in the stock game, and they probably shouldn't, but the option will allow for more variety and greater ability for the creativity of the Users to flourish.
I'm glad to hear the change in intel, but please put a direct link to it on the main screen like tech in SE4. Hiding it in diplomacy can be a bother since it adds in an extra click. Perhaps from a UI perspective you might allow a right click on an enemy ship/planet/whatever to link to an option to target an intel project against that particular thing. With SE4, I often have to write down the name of the ship or planet that I want to target.
Spice up ground combat to include options to train troops (have it mean something). Ships have experience, so should troops. If at all possible, use the SEIV space combat system for SEV ground combat (or even the SEV space combat system if that is doable)
Empire wide facilities similar to system wide facilities.
Another alternative to population/cargo transport micromanagement is to instutite an invisible cargo system whereby the user selects a planet and then selects a destination, the computer calculates a time penalty to figure out how long it takes for that cargo/population to move to the destination (or it could just be a user defined flat rate of X turns by warp point distance). Perhaps it can be constructed so that in game, players can build invisible "transport fleets" that allow for greater amounts of cargo to be moved, or at faster rates. There are quite a few options with that. The point being, you handle the resources in a similar manner- space ports magically dumps all your resources whereever you need them in SE4, so why not apply the same logic to people and cargo in a slightly different manner.
The above will help decrease the micro-management that can detract from some of the larger games (or when you have umpteen races)