1) It isn't really a bug.  You can design some ship's say at the beginning level, middle level, and it's stompin time level.  Then work on researching the needed Techs in the game to actually build and deploy your custom ships.  Once you save a custom ship design, it's always available to you.  You just can't build it and deploy it until you have all the Techs.

This implementation IMO is very helpful because you can learn what's available for your ships and what sort of offense and defense is possible without having to first research everything.  It makes it easier to learn playing the game.

2) Any ship you currently can build in game you can also customize in the Shipyard, possibly improving the Tech on it to add some armor or shields as well as more powerful offense.  Believe me it's a lot of fun to research a higher level of beam and shield and place it on your small defender in the early game and then watch the opposition crumble when they're now out gunned. 

The Shipyard is your friend in this game.  Just watch the cost and maintenance figures it shows you as well when designing your invincible fleet.  Powerful ships are expensive to build and maintain.  You need a a number one economy ranking to have a number one military ranking for very long in this game.  Very realistic if you ask me.

3) the ship "Focus" will allow you to start with a stock ship and remake it to your liking.  Make sure you rename it or it's new higher tech will preclude it from being available to you in future campaigns until everything needed is researched in game.

The computer AI players only can use what is in their stock shipyard or, what's traded to them.  They don't customize their fleets.  Just be careful what you give to an ally though, they might just use it on you!

No, this IS a bug.  I'll detail the circumstance I'm familiar with, but maybe the underlying cause applies elsewhere.  I'm not sure if the fix is something that can be done in the data files or not.

We'll use the ship, "Destroyer M1" as an example.

Destroyer M1 requirements:
Ion Drive
Large Scale Building
Laser III
Superior Deflectors
*needs more miniturization

*now this is where the bug comes from.  It's fine to SAY a ship needs more minturization in the tech tree description, but it has to be enforced somewhere in data or code as well.

Now, with the handy dandy Focus of Laser 100% and Deflectors(?) 100%, I could build this ship by selecting it in the shipyard as an automatically generated design.  I have indeed researched the prerequisite techs, EXCEPT the required miniturization needed for this to work.  I have only researched to this point, Basic Miniturization: +10%.

Here are the ship stats the auto design came up with:
Beam Weapon Attack: 9
Deflectors: 3
Speed: +1
Hull: Large (size 80 +10% = 88)

If I try to build this ship in the ship designer by myself, with BETTER lasers (IV), I can only get:
Beam Weapon Attack: 9  (9 x Laser Mark IV @ size 9 = size 81)
Deflectors: 1 (1 x Superior Deflectors @ size 5 = size 5)
Total size = 86
Hull: Large (Basic Miniturization +10% of size 80 = size 88)
So, used size/max capacity = 86/88
No room for an engine here, and I'm missing 2 to the deflector stats.

Now, to build the ship that was designed for me by the computer, I would need a hull size of 113.  That is with the superior Lasers IV used in the best I could come up with.

Here are the various hull sizes for a Large hull with various miniterization techs:

Basic miniterization +10%: 88
II +15%: 100
III +15%: 112
IV +15%: 124
V +20%: 140
VI +25%: 160

So, in other words, I would need to research up to the FORTH miniterization level to fit all the components to match the computer design.

I should NOT be able to build this vessel, but the auto ship design feature puts it in my buildable ship set anyway, THREE techs short of being able to do so legitimately!

That is a lot of research saved, no?

It's funny, I just noticed this today, and here there is a thread about it.  I've experienced the same thing, and I can't seem to rationalize it as not being a bug, and a fairly serious one at that.

Additionally, the "*needs more miniaturization" message never ever goes away, even if you have researched every miniaturization tech in the game. 

Eh?

Still, it's telling me I need more miniaturization to build a ship that it already lets me build, and that I really shouldn't be able to build.

It seems such a significant issue, I am surprised that this thread is the only one I've found on the internet that's discussing it.  What are we missing?

The only way I could see it being a "feature" is if it's some kind of difficulty-level slider...  But then again, there is no such slider, so, there goes that theory.

All of our reports on here seem to be discussing the Destroyer.  Is this the only stock ship for which this occurs?

Maybe this gets fixed (or explained) in 2.0? 

If I understand things correctly, the computer players most definitely create their own designs. With the most recent updates, I've even begun seeing some interesting experimentation where an enemy ship design actually includes a secondary weapon (e.g. missles) that targets an unpopular or unused defense type.

Also, if I recall correctly, a major benefit of using the Max CPU option is that the computer updates its ship designs more frequently. I'm pretty sure that doesn't mean just picking from a stack of templates, but even if it does, the stack must be pretty big given the variety of designs I've been seeing in late DA and TA.

At first it seemed that way to me too but, I've discovered that in order to have some really effective ships with torpedoes or rail guns, I have to build often build them.  While it's true a stock ship should be preferred when available sometimes they just aren't.

1) It's a bug, and  a bad one that I've noticed as well. There's very little point in having a ship design screen if the defaults are superior to what it is actually possible to design. I've noticed there is a rather strange attitude that this bug should not be fixed for some reason. I could see the arguement for having the defaults be the best possible design with available tech (it surely can't be that hard to, for instance, get the computer to design a ship with the maximum possible attack value), but it makes a mockery of the whole thing for it to break the rules. I really hope to see this fixed.

2)It does become less of an issue in the later stages - the default designs seem to be very one sided ships and poor on survivability. It may also be that the bug is related to miniturization, which will become less pronounced as you get more tech. However I do find it does make ship design a waste of time at least until medium hulls and second level weapons/defenses are around.

I thought that this bug was already fixed? without owning any of the miniaturization techs will researching just the first upgrade the design as i am sure my ships have upgraded (might be better to wait for some of the better weapons/defenfences to try it)

Well, you don't know what you're missing!  (Specifically, lots of free tech!  )