as co-author, cannot omit Improved Races - changes game and makes it harder on many levels (depends of how many features you enable)
ship rebalance mod + cmod - matter of preference, but I cannot play without 'high hulls' now. At first, it seemed bit ridiculous, but now it feels JUST RIGHT. M1, M2 ships have hulls comparable to their shield (8-12 mln hull), making them really, really hard to kill for fighters. Destroyers feel really powerful, not made of paper, and they dont blow up just after their shields are gone. Also, it fixes almost all OOS fight issues - there is no way that any ship can unload enough firepower in 30 second OOS tick to insta-kill any huge ship. OOS rebalance is not needed with this installed. + ton of new ships (especially rusty Khaak ships have been slighly updated lately) and MANY BUGFIXES. THreat this mod as huge, unofficial path for X3 (ie it contains factories that were missing or broken, fixes broken ship models etc)
If you use those, you'll need MARS goblins for repairing hulls and all other tasks. Goblins make game much more pleasant, and are just funny to watch

Lucike scripts for trading, fleet management and other stuff. CODEA/CAG/Prospector/CLS are must haves. What Lucike plugins give you, is pilot management that adds a lot of life and makes gameplay much more rich. You can use MEFOS instead of MARS