For ATO, your choice is limited, but the works are solid. If i was to play the ATO in SH4, these are the first two things id look into:
Operation Monsun
KiUB Kriegsmarine Interface for UBM
For the PTO you have two supermods:
Real fleet boat
Trigger Maru Overhauled
And one major campaign mod. Required for RFB, optional for TMO.
Run silent run deep
Now that all said, Im a fleet boat fan, and pefer the PTO, and have spent the last few years busting my balls to improve Sh4.. and yet here i sit wanting to play SH5. That must say something about it. Although, SH4 is just work to me, stopped being fun awhile ago. I recieve no joy playing it anymore because i ive spent too long modding it. *shrug* So take that last minute endorsement of SH5 with a grain of salt.