Dunno how an X3 Succession Game will work, if playing with mods you'll need to have every future player have all said mods/scripts installed or else transfer the entire 4-5GB game folder around.
As for TC vs AP, unless you're against the whole "war sector" thing AP is definitely superior. Stock market is a bit gamey, so I wouldn't recommend it. Just remember to pack missile defenses or be prepared to freight scan anything you might be attacking.
As for you asking about mods, I highly recommend the following:
NPC Bailing Addon: For better (not so much to be iffy though) bail rates.
Salvage Commands and NPCs: Ties in with above.
Pirate Guilds: So pirates are actually useful aside from scrap.
Yaki Armade: Like the above, except for the Yaki.
M.A.R.S. Fire Control System: So turrets won't suck terribly.
Docking Lockup Fix: Because the AI is stupid.
Terran Revitalization Project: A set of scripts which add more functionality to the Terrans, and helps their economy not be a complete disaster.
Community Logistics Software: Because CLS/CAG > UTs.
Other Possibly Useful Scripts:
CODEA WS: For better command of fleets and carrior squadron maintenance.
Anarkis Defense System: Pretty much CODEA Lite.
Remove Rocks from Universe: In case we have FPS issues in rocky sectors.
Convert Passenger to Marine: Let's us turn a passenger into a marine using space fuel. (In case we have a "misunderstanding" with all Military Outposts).
Marine Trainer: Allows marine skill training on any ship that can carry marines (For a steep cost).
Marine Repairs: Ships with marines will slowly repair themselves (And slowly train the marines).
Capture Stations: Allows you to capture stations via boarding (Only number of marines matter, skill is irrelevant.)
Station Repacker: Works with above to allow yoink-ing of stations.
Stuff for Shiggles:
Ring of Fire: Because vanilla lasertowers in TC suck.
Combat SQUASH Mine Launcher: Fun if one can obtain reasonable quantities of SQUASH mines.
Auto Beggar: Exactly what is says on the tin.
Cargo-Beam: Allows one to "beam in" a drone/spacesuit/cargopod using a transporter device. (Direct Link!)
If you use CODEA, individual fighters can be given named pilots and gain skill levels (and thus survivability) over time. You could try a community fleet using it.