Some of what I suggest now will be things that have already been mentioned, but I don't want to cherry-pick those out of my overall post, so we'll just have to deal with the repeats.
I like the concept of a certain randomness in research. Not constantly...but you research a technological concept and sometimes it turns out different. Maybe not as extreme as researching a laser and getting a planetary improvement (although maybe once in a few dozen techs that might be ok), but rather researching a laser and getting a new kind of laser that performs differently than usual...say a drastically different (and preferably useful) balance of output vs cost vs space, etc. Maybe...1/3 of the time that could happen?
An option to be more methodical in research than usual. If more randomness were introduced to the system, then creativity could allow for slightly quicker research with more random results...while methodical could slow it down a little but ensure that you get what you're looking for.
A more broad, but smaller basic tech tree. Certain techs should just be endemic to all space-faring races...but there don't have to be that many.
Larger and more beneficially specialized racial tech trees. There should be a far greater separation in specialties between races, and more thought should go into how an advantage or deficiency in one category of tech affects their capabilities elsewhere. Certain combinations of advantageous and disadvantageous tech categories in various race trees are borderline stupid.
Larger and more beneficially specialized alignment tech trees. Alignment has almost no point in the game. I always choose neutral solely so I don't have to upgrade the class of my colonies. Good and Evil are practically worthless, their defensive and offensive bonuses far overshadowed by the configurations of weapons and defenses I place on my ships. The inherent bonuses of each alignment should be more closely associated with their ethos, and more broad in application. The number and nature of techs accessed through alignment should also be much, much greater in number.
Something like...basic 1/4, Race 3/8, Alignment 3/8.
Do away with the nonsense that missiles ultimately end up doing the most damage relative to space...etc. I understand the purpose behind it...but it only leads to ships running around with nothing but missiles because beams and cannons are almost stupidly useless.
On a note only tangentially related to tech...add the feature of power output/consumption to ships. Just because you've got room for a nice big doom ray, doesn't necessarily mean your ship can power the thing. That could create a further method of divorcing the similarity between beam, missile, and cannon weapons. Missiles take little power, cannons take some, and beams take much...though with defenses it would be armor, PD, shields in terms of power consumption. Researching the power plants in the tech trees as we know them could be expanded more, and also count toward how much power your ships can put out for weapons, defenses, and engines. Thus, researching larger hulls might not always do you any good if you don't have the power to fully outfit their available space. And relying solely on little ships for the game wastes power. Unless power plants for ships are modular like weapons and such.
