After thinking back on the final battles of CT and CC, I can see a vague pattern in the physical design and LOOK to the final bosses.
In Chrono Trigger, no matter which way you do it, you go through an outer shell and face a very lean, mean killing machine that seems like it's got some kind of awareness or intelligence.
Likewise, in Chrono Cross, facing the Time Devourer, one can see the basic shell, and another entity inside it, Schala.
Now has there ever been any thought as to the relationship between these looks? Could it be that the outside of Lavos is a kind of "armor" housing a sentient being inside? Is it possible that the Lavos one fights inside the shell (not the accumulated DNA creature) is some sort of sentient being controlling Lavos? Or is it being controlled BY Lavos?
Insiide the Time Devourer, Schala seems to be in some kind of stasis, where as inside Lavos, this being is obviously very awake and in control. Could Lavos latch on to other beings as a fail-safe of survival? Why bother fighting for your own needs when you can force someone else to do it for you, the being inside the Lavos shell is obviously connected, "bonded" with Lavos. Should Lavos die, it dies, all Lavos has to do is sit there and the thing on the inside does the work for it.
This COULD be a reason why Time Devourer is so small. Schala is very powerful and obviously hasn't been completely taken over yet, she's still able to be saved. Perhaps the being Cronos and friends fought was the unfortunate victim of Lavos, too far gone to save?
Just some ideas throwing out there.