Err, doesn't initiative work in such a manner that the lowest initiative moves first?
Err, maybe. *shrug* If so, set system bodies to 0.
The thing is, why should missiles be unable to be intercepted just because of their high agility?
They shouldn't. They should be harder tp intercept the higher their agility is; hence the bonus to initiative.
One can manually plot a course to intercept where they'll be in five seconds, but it's a pain in the ass to do, so I figured one should be able to have the game calculate where to go for them. The game already presents the player with all the information the game would need (Heading and speed of the missiles) to make the calculation, so why not take it one step further?
Because it's poor programming practice to write an exception. It's also extra work. The 'move an object' code already exists; the problem is that it moves all the system bodies first, then all the ships, all the fighters, and finally all the missiles. The artificial rule 'this class moves before that class' leads to all sorts of problems, not just the particular case of 'I want to hunt down missile salvoes with my fighters.'
Anyways, it wouldn't work the way your asking for because Aurora doesn't know how long the next increment is going to be until you push the button to advance time - you'd need a separate input box where you tell Aurora how much the next time advance is going to be (which Aurora needs to remember if you have 'Automated Turns' checked) and uses that information to calculate where to put the waypoint it then tells your fighter squadron to move to . . . AND Aurora would need to keep track of that information in case an interruption occurred during the specified time, and then recalculate all the values with respect to the subpulses that had already been carried out - PLUS write a whole bunch of error-catching code in case the salvo being followed ran out of endurance, lost guidance and self destructed, was shot down, passed through a jump gate or black hole or hyper limit, or worst of all, split up. (If the salvo you're following divides itself to go after four cruisers, what should your fighters do? What happens if there aren't enough fighter to follow every mini-salvo?)
Your problem is "The Follow (and Move To) action is broken because of the sequence of play; fighters always move before missiles and thus can't be made to Follow a missile salvo at a range shorter than (missile speed x 5 seconds)." The solution is not 'write a new order that does what Follow does but only for fighters chasing missiles' (as Steve pointed out elsewhere, there is already 145 different fleet orders) but rather 'fix Follow (and incidentally Move To) so that it does what it's supposed to do for any class of unit following any other class of unit'.
All of this, of course, is assuming Steve even wants it to be possible for fighters to move after missiles. I don't remember his reasoning for setting up the Sequence of Play the way he did - I'm not sure he ever considered the logistics of fighters chasing missiles - but I seem to recall something about ships moving towards missiles not triggering point defense properly. Basically, ships could inadvertently 'ram' missiles, and doing so not only negated point defense but upped the missiles hit chance significantly.