Alright N00blers, I have had the solution for this problem for years and its depressing no game maker has picked up on it yet because I want to play such a game. Originally this was intended for RTS type games, but it can work in any strategic game.
The basic premis is that there are not any fixed techs or units in the game. There are provided techs and units you can use so you do not need to make everything, but you are not limited to what the game ships with.
Now how does this all work? With a point system, say like Hero systems or GURPS. You buy technologies with points, you make units with points, you make improvements with points. Players decide what powers they want in some object, such as armor, hitpoints, speeds, etc. and then the game computes the research cost and production cost for you based on formulas. Similarly you can make ‘parts’ like this, such as heavy lasers or turbo lasers. You reasearch these, and then when you are making a ship you can staple on some reseahed weapon and its just added to the cost.
Certain technologies and power advantages have others as prerequisites. For example, before you research dimensional travel, you need teleport, and to get teleport you need matter-enery tranmutation, etc… This is your tech tree. Also you could include a tech level (to mark technological epochs) which would forbid certain technologies until you reached the preqrequisit epoch. This might also can be used to give discounts on lower-epoch units, or enforce a rule allowing you to make stuff from +1 epoch (you capture some tech, you can make it, but do not understand how it works) at an increased cost and size.
Throw in a graphic editor that featuers some modular graphic design and you are good to go.
Now my favorite part of this whole system is in multi-player when you see an enemy unit and you have NO IDEA what it does. It would add a whole new level of these games. You go into someone’s base, you have no idea what structure does what. You might be attacking a building of minor or cirtical importance. Finally in game, if you need a unit to counter some other guys units, you can always design one, research it, and build it.