Might be a feature for the roadmap. I'll add it to it.

I agree with Gypsy2299, as long as I don't click on the next action Icon (bottom right corner) when it's yellow, the game will allow me to do whatever I want without advancing to the next turn - 

Yes, I'm talking 4.  It doesn't do auto/continued moves until you hit the end turn button.  It then does the auto/continued moves.  If any of those ships you have on auto or multiple turn movement orders encounter anything, you no longer have the option of reacting to it before the AI goes even though technically it was still your turn while those moves were taking place.  If any still have movement left for any of these continued move units after they finish, you then have to move them.  Unfortunately, after you finish that last order, it doesn't then do another end turn button.  It just goes.  3 did have an option to enable that second end turn button (really it was disabling the auto end turn option) when I was actively playing it. 

This really is game breaking for me.  I have already lost 3 colony ships due to them moving after the end turn and not giving me the opportunity to wake a nearby ship/fleet that I placed to safeguard the area for just such a possibility.  I shouldn't have to manually move each unit every turn to avoid this.  In this same vein, why don't the auto explore, survey, and continue movement units wake up when spotting an enemy so I can use the rest of their moves to move the other way or attack (if capable)?  I thought they were trying to get away from all of the micromanagement.  Why have multi-turn movement and auto explore/survey at all?

Now possible solutions other than putting back the option for the second end turn button would include having the auto/continued moves occur at the start of your turn or providing a move all function that can be done before hitting the end turn button.  Perhaps the first End Turn button could just be a blue move all button then the end turn button appears after all units have been given orders.  When I hit the end turn button in a turn based game, I expect that it's now the AI's turn - not that I will then have more of my own units move.  

For now, I guess I'll either micromanage my moves or rely on reloading a lot, which I don't like to do - feels a little like cheating. 

@SchismNavigator Thanks for your patience and listening.  Maybe some of these suggestions will help.    

Yea I think the idea here is that if you hit the end turn button, that is the end of the turn.  It's not doing that automatically, the player is pressing the turn button.

I agree with chazz_play. The way ship movement is processed with the End Turn button right now is not good.

What will happen sometimes with me is this: I'm out exploring a new sector with a probe. I notice during the AI turn that a pirate/alien ship moves into my probe's sight. I make a mental note that I will have to move the probe away from that direction to avoid running into a nest of hostile ships. During my turn I forget about this because my probe is in a very distant sector and I have so many ships and other things to manage. Then I get the yellow arrow telling me I can advance my turn. I press it. Then because I had say 5 or 6 moves prescheduled on my probe, my probe moves into danger before I get a chance to tell it where to move. I can still move my probe away with my remaining moves, but at that point there's a good chance it's just toast.

Another thing that can happen is you can get locked out of making important end-of-turn decisions. Let's say you're expanding and you don't see any planets to colonize, so when you get the prompt to select shipyard construction, you opt to build another probe. Then when you run out of things to do, you hit "Next Turn." Your probe has some prescheduled moves, so it takes them and asks for more instructions. You tell it to keep exploring. It immediately uncovers 2-3 Paradise worlds. It would be really nice to be able to go back and switch your planet's production to "Colony Ship," but the turn automatically ends and you've ended up spending a turn of manufacturing on a probe you aren't going to need right away.

I think the "Next Turn'' button should have two phases. The first phase would be just like it is now but it would say "Advance Turn." The second one would be a red arrow (instead of yellow) and it would say "End Turn." Ideally, you would be prompted to select your Colony/Shipyard projects and Survey rewards only after all your units have used up all their movement points.

Side note: Pressing space bar or "passing" your turn with a ship should just forego using movement points rather than depleting them. Currently if I choose to pass a turn, I can't reverse my decision.