Hi Matt,
the GPT (General Purpose Timer) supports just about all the functions of all assorted timers Renesas previously hosted in the H8S and RX families.
Two-Phase (called Phase Counting Function) and Three-Phase (UVW) decoding are definitely supported by the GPT.
The complexity of this timer however makes the User Manual difficult to read.
It's to be hoped that Renesas will release an Application Framework supporting Motor Control functions in the near future.
Cheers
Lou