The latest stable patch (r16134) includes a number of new techs. (Here's an updated tree jpg.)

Connected to these new techs are some new rules around just how captured ships are handled. Captured alien vessels will no longer automatically become part of your navy. Instead, you'll need to decide whether to scrap them for resources, or reverse engineer them; much as you would if you encountered an "alien derelict" system special.

However, there are 2 techs that can change this. If you've researched "Xeno-Engineering" you'll have the option of integrating the captured ships into your navy. And if you've unlocked "Quantom Decryption" you'll actually be able to take control of enemy craft mid-battle, potentially turning their guns against the remaining enemy ships.

(The missile retargettng tech that we all agreed was a good idea is also now in game: creatively named "Retargeting Systems".)

(Similarly, auto-repair systems are also now in the game; though they're missing graphical assets, and could probably use a bit of balancing/playtesting.)