I always liked the way Alien Legacy Handled research.
You'd discover items or encounter events that would unlock research topics each topic had a cost in the six different science fields. Once you paid that cost it would take a period of time before you received the results of the research.
For example your settlers might have found unusual mushrooms growing near their new settlement. It cost 50 biology points, and 25 chemistry points to research the mushrooms and they result is you can now build advanced hydroponics chambers giving you more food per turn.
A rare crystal you find while exploring a moon might let you finally unlock phaser technology for your ships.
Discovering and researching Naqudria might allow you to produce hyper space engines small enough to fit on fighters.
It was good because your exploring and events shaped your research paths and technologies you unlocked.
One game I played I think it was War Of The worlds required the enemy to use technology against you before you can research things. For instance before you could research air filters your enemy had to start using bio weapons against you.