Ive said this on another thread before but I much preferred ToD over ACiT.
Heres why:
Planets: I thought ACiT didnt have near enough planets, ToD had loads. I know ACiT had the free roam in space thing, but i didnt like that at all. Then there was the galactic map in ToD, much better than the one in ACiT imo. The Great Clock in ACiT is a huge point in ACiT's favour, but its not enough to make up for lack of planets elsewhere.
Graphics: I personally overall preferred the ToD graphics, its very close, but ToD just about wins for me. There are several areas where ACiT graphics were better (Great Clock, the water, weapons etc). But in the end its ToD graphics for me!
Gameplay length: For me ACiT was just too short, not much else i can say here.
I will say this though, the clank gameplay in ACiT was just brilliant, and I loved the Great Clock 
So there you go, thats my opinion anyway.