Regeneration ability 'bug' ??

I don't think it is a bug.

When you refit a ship, and the engines are upgraded, Even after the engines have been repaired, the ship will have a movement of zero (0/15) because the movement points are calculated (added) AFTER the engines are repaired. You need to wait for 1 turn processing for the movement points to be refreshed.

I think what you are experiencing is:

Ship with 15 movement points.
Ship takes engine damage and can only move 9.
Ship repairs engines but the repaired engines do not have any movement points, because movement points are refilled during turn processing.

There is one minor problem I see with everything self-repairing.
Where do you keep the spare parts?
With stuff like a Repair Bay, you have stuff that can repair and possibly recycle and rebuild stuff, but a repair team is not going to have such a luxury.

Even in Star Trek, with replicators and whatnot, there is going to be a point where a ship is going to be so badly damaged, that it's being held together with duct tape, chewing gum, and a prayer, and that all the repair teams in the world aren't going to help at all.

One thing that would make sense, if 'repairs' costed supplies, to represent that they are making the repairs with what they got on hand.
That's apparently how Organic Armor works, it only is supposed to heal itself if there are supplies remaining.

Also, due to the complexity of engines, while a repair crew might be able to patch it up, there is the problem of replacing damaged components that simply cannot be repaired by a handyman with a really big tool box.
Another example with Star Trek, a Warp Core requires Dilitium Crystals, if those crystals get ruined, and they have no replacements, they got a problem on their hands.
Also, there is more to fixing things than just slapping in a new part...

Captain "Engineering, those engine repairs are supposed to be done by now, why don't I have full speed yet!?"

Engineering "They are repaired, Captain! But the impulse driver coils got knocked so far out of allignment and sync that we are lucky we got them alligned enough to even work partially!"

Captain "Then get them properly alligned and resynced before the enemy gets in Ripper Beam range!"

Engineering "Sure, captain, can you tell them to stop firing at us for a few minutes so we don't have to do the equivilent of building a house of cards during an eathquake?!"

That and maybe such things as speed loss are only 'fixed' after battle, or perhaps only with proper repairs from something that can do repairs, such as a Repair Bay or Space Yard.

well hes talking about organic armor and other components, I would hope he made them all organic components and not self repairing everything...(non organic self repair on everything to me is...well I guess I could see it on like a Borg cube or something but there would have to be a reason for having it, and use this selectively, (and responsibly =p) and not just to make an uber ship

There might be a way around it. There are some possibilities to alter speed in combat. (hyperdense globula from organic tech does this for example.) I don't know if there is possibility to counteract this, but something that works like shield regenerator might be what you are looking for.

Perhaps adding inverse effect of the globula to the engines would speed up the ship in combat? But can it be done? And would it actually speed it beyong the original top speed.

Afterburners alter ship speed to, but i don't know if it can be done just by a component ( you would have to check repair state, then compare the generated thrust to the actuall movement, and then fill up the gap .. )

Remember : Pillage! then burn.
- Cpt. Kaff Tagon