A hotkey to allow all units with orders to move when pressed would solve this one quite nicely.

I agree with the OP. Having units move at the beginning of the turn is a little unintuitive.

When do units move at the beginning? 

Actually, they don't, it just looks like they do.

1. Give a long move order.

2. End turn.

3. End turn again.  Your guy will not move.

4. End turn again.  Now you see him move.  The game is actually moving everybody who hasn't moved, then ending the turn, but it looks like they are moving at the beginning since the movement follows the clicking of the button.

Confusing.

It's the same system used in the Civ and GalCiv games.

At 3 your unit should move. It should have it's movement back from the first end turn and then spend it on the 2nd end turn. Not sure how it can be seen as at the beginning since they move before the AI. Actually moving at the start of the turn would be bad, because then you wouldn't be able to make changes. Maybe it's backwards in tactical combat, but because of a bug that can force you to autoresolve, I don't move outside my range in tactical.

I think I just was confused and got it wrong how the units are moving. Either that or it changed in 1.07.

The unit moves are definitely counter intuitive - agree on a button and/or more clear movement.

Also, ship movement animation is ridiculously slow - locks me to viewing the ship while I wait for it to plod a few squares.

Units do move at the end of the turn.

Not sure why OP thinks they don't.

For the love of god, this please. 

I agree with you, but also with the OP's observation that the current system is a little off-putting.  The whole thing as is just looks a bit awkward, since I don't see enough visual cues that my unit is really going to move.  Once I've finished with my active moves, I'm ready for the end turn button, but since my pre-programmed moves haven't been executed yet, I keep wondering if the remaining units really have orders or not, and often end up clicking on them to double-check or even redo their move order, which defeats a lot of the reason for setting a long move to begin with.  I realize some of this is just me learning to adapt to the engine, and unlearning habits from other games (at least Civ has a "Contiune move" button), but if other people are getting bothered by this too, maybe the interface needs a change to something a bit more intuitive.

I'm sure the SD guys are tired of hearing "but Civ has..." but one thing I liked a lot in Civ 3 (and ETW and probably zillions of other games) was when you tried to move a unit further than it can go in a single turn, it tells you how many turns you will need to wait for it to reach its destination.

Bingo.  Civ 4, you get a nice line, showing where every move will stop, and how many turns in all.  This is enough to reassure me that the game has understood my instructions and is showing me the path it intends to take, further reassuring me that the game will indeed accomplish the task I set it.  If I should worry about it, another click on the unit shows the path again.  Here, there is no path shown, just the destination square.  If I click again on that unit, and the destination square is not on the screen, there is nothing telling me the unit is on a long move.

Just showing the intended path/number of turns would probably go a long way to clearing the move thing up.  Still, this is a basic usability issue that should have been addressed a long time ago.

As I already did my suggestions to the devs - find any 13 years old kid and let him play for 10 min; he will how to remake the controls. With the current controls it is boring click-fest.