The Second Edition rules are in many ways the same as the first edition but not 100% compatible.
The biggest difference is that ships go a lot faster. This will change the tempo of older missions. I will post an update that tells how earlier missions need to be modified to accommodate these changes. The campaign aspects of the classic expansions remain untouched.
The species, special abilities, modules, equipment, and rules from all of the expansions have been either been re-envisioned and included in the second edition or intentionally discarded.
In the original game, the Hull Stabilizer and Tractor Bay were modules. By second edition, they've both been demoted to Cargo Bay Items along with the Fighter Bay. The Fusion Cannon has been turned into a Cargo Bay item that allows your Cannons to be configured in "Fusion Cannon" mode.
As far as physical components, the second edition uses an industry standard 1" square grid for modules as opposed to the original edition's .7 inch grid. The reason I settled on .7 inch originally were to fit the game on the table and be able to put 6 modules on an 8.5x11" sheet. Going to the full inch required a fundamental change (Engines and Cannons can now be used with used markers on them at a penalty of -3 each). This means you need fewer total modules and the ships now fit on the table.