I'm totally against detailed tech research, unless it's really small-scale, like in deadlycairn's minigame idea. But in grand-scale strategy games, generalizations are simplier, and so, easier to implement. They're somewhat like ascii graphics, in the sense that you don't need a hundred people working on inventing new wacky names for every little tech, while giving generic name like 'cannon V' or 'advanced infantry' lets the player's imagination do the rest. Naming and researching every srcew and every test stage is meaningless, mindbogging micromanagement and gives rise to silly situations, like "Oh, I've got 'super-duper plasma gun', now I'm researching' 'super-duper pg with blinking diodes'".
There are some games that did the research(and/or tech implementation) aspect almost right, namely: MOO2, Europa Universalis and Hearts of Iron series. If one combined these three, he could get a system close to ideal(in my opinion, of course).
MOO2's best innovation(as somebody mentioned before) was the percentage-to-breakthrough system. I'd go as far as allowing a small chance of succes right from the start(logarythmic scale, perhaps? so no 100% chance either). Also, It'd be probably a good idea to hide and randomize the tech cost.
This way, you can have accidental discoveries; prolonged funding of dead-end ideas(each turn you're unlucky); the common-sense rule that the more you work on something the higher chance of achieving the goal is also satisfied; if costs are randomized and hidden, you don't know in advance which tech will be easily done just because you've played the game before(there could be a general indication like 'easy' or 'difficult' etc.), also this would simulate:
Acceptance rate
.
EU's foreign influence on your research is a great idea. Basically, if you're bordering a country with higher tech level, you get free research points. More if your culture/religion is similar, if there's high advancement levels disparity, and if there's more than one such country. This simulates the "we need bazookas to counter their tanks" concept, how one invention stimulates another, as well as the free flow of ideas(with religious/cultureal restrictions). Would work well for any kind of 4X too.
For added 'realism' one could get extra bonus 'science points' to combat techs when at war(or better when actual combat took place) and reduction in civilian tech bonuses(closed borders etc.)
While EU did away with complex tech trees altogether(just 5 or 6? techs to improve), HoI had a bit more 'juicy' system. You could develop(it's IIWW) generic types of units e.g. infantry, tanks, fighters, short and long range bombers etc. While some of them had names to match the histiory, they were simple upgrades of the previous ones. Basically, you had (almost)every type of unit, available from the start, which you just improved during the game.
This upgrades system is woth noting: you spent resources from your pool on a day-by-day basis to refit old units, so you didn't have to disband the old '36 infantry. You'd just let them fight and, providing the supply lines were maintained, bit by bit your army would get modernised.
Ships, being large hunks of metal, were unreffitable, these had to be scrapped, but were still useful even when outdated, as a ship is a large investment of time and resources - by analogy, this would work great for 4Xs
China's economy today is an excellent example of the variation problem(...)
this can be easily done too(it had been done before). Your teritory/planet has varied levels of industrial capacity/infrastructure. You can't build you newest tanks/spaceships where you've got no ability to do so, but you can easily commision a starport, or improve said infrastucure to change that over time. And this could cost more/decrase happiness to reflect the cultural inertia of a given society.