A long time ago, there was a well known bug, sometimes called the speed bug. This would occur sometimes when player ship speeds were not being calculated the same by each client computer in a multiplayer, the effect was that ships would appear to be out of sync, jumping around all over the place. To correct this, it was necessary to have all ships begin at speed zero, or, if already in mission, have all ships come to a complete stop for several seconds.
This bug was fixed with one of the last patches for OP and no longer exists, it is no longer an issue and we have not seen this bug again. One of Dave's patrols (the one with the pirate) starts you at speed 15, I think, and never had any issues.
The only real issue now about starting a mission at speed is the power it takes to load up weapons. Ships that require more power to charge up weapons have to slow down more than ships that don't need as much. Ships that use lots of drones, for instance, will be able to maintain their speed thus getting to the enemy quicker, thus reducing their mission time. The question then, is by how much time do they save, and what impact will it have on the game. The players are set far enough apart that even plasma races will have all weapons charged, but its just the mission time that might cause a problem. So this needs testing, just how much of an advantage do droners have over plasma in this case. Perhaps some of the regular plasma and drone players can test this out?
With regard to capturing the freighters making it too easy, I can add more marines to each freighter from within the script, remember the default AI marine levels are set by the shiplist, players always carry maximum marines. While destroying the freighters on capture solves the problem, its unrealistic I never did like that aspect of the old convoy raid myself, it seemed silly. But if everyone wants the freighters to blow up, I'm happy to make this happen. Adding a few extra marines would slow down the capturing process, and make a player use up more marines, but still not completely rule it out as a ppossibility. Irrespective of what we do here, a player who plays the mission enough times will eventually find the best tactic for completing the mission as fast and as efficiently as possible. Some races are better at capturing than others (eg. Klingons), others are better at using weapons that don't require much power (eg. Kzinti) etc etc. and I have been reluctant to disadvantage any racial flavour that each race has. The idea I'm trying to do here is not make the mission a cakewalk, but reasonably challenging enough that it doesnt get boring each time you play it, but must still be winnable at least most of the time.
Thanks again for all the feedback, and thankyou to everyone who has played it so far, please keep the feedback coming, both good and bad its much appreciated.