Yes, I know of these problems.
The incorrect population allocation bug is a known one, but is thankfully relatively rare. I believe Mike is still trying to find the cause of it, so there isn't a fix available - yet.
The shiplist that is currently implemented is going to undergo a major overhaul soon - in fact, i'm going to be doing this overhaul myself. When I do the overhaul, the obsoletion system will make ships that are two stages old obsolete - so, for instance, gaining the ability to build Sovereigns will render Ambassadors obsolete and will remove them from the build list. You will still be able to build Galaxies at the same time though. The only exception to this is with non-combat ships, where you will ONLY be able to build the latest version. As the non-combat designs can't fight, you won't really want the old designs anyways.
I know that there are some people out there that will want to be able to build NX's at the same time as Sovereigns, and that WILL be possible - you will just need to know how to use the game editor. Once the game is complete, I will post instructions on how to do this (I can send you a PM now if you wanted), but the built-in auto-updated causes a problem, because it will recognise your changed game files as being "old" files - and will then download an "updae" to bring your changed game files back up to the standard. Therefore, you will either have to keep editing the game to allow the installation of legitimate updates, or you'll have to stop updating the game.
_________________"Anyone without a sense of humour is truly at the mercy of the rest of us."