Please use paragraphs to make it easier to read your post.

Apologies if it is the carriage return thing.
These sound more like feature requests than bugs; I think it's a little unfair to call them bugs both because there are people who will disagree with some of them (including myself) and because it unfairly paints the devs as sloppy. Some specific comments....
2) I'm not sure what you mean. Phasor 3v2v1 etc. mean that you may be able to design ships with more powerful beam weapon attacks. You can't have civ 4 like descriptions of weaponry because of the ship designer. I agree though that it would be nice if it was easier to navigate though. (maybe zoomable interface).
4) I disagree. I think it would ruin the tbs feel if tech could become godlike.
5) Personally, I do not need to actually see the type of invasion to envisage it.
6) Again, I think this would ruin the tbs feel. BTW, are you aware that you can attach multiple engines to a ship?
7) It seems a bit arrogant to say "it doesnt always work to the extent that i propose you made it for". It seems more resonable to say that your vision and the devs' vision of the role of espionage are different.
9) Not sure what you're saying. (Exceptional circumstances aside), I build a starport on every planet I own (though I'm considering changing this for strategic reasons. I don't think it is unreasonable to have Galactic Wonders and Trade Goods built only once.