There will be several steps. First - yes, graphics update, proper networking, raising/removing some SMAC limits, fixing bugs, speed improvements (for example, multithreading). There will be few balance fixes aswell, notably - probes will be nerfed in several ways because they are way too overpowered in multiplayer. Also secret projects will auto-cancel and refund minerals when somebody else completes it (instead of allowing player to keep building it forever and then switch to something he just researched to insta-finish in 1 turn). There will still be options like 'Legacy Probes' for those who truly want old behavior, but defaults will be without overpowered/broken things so that multiplayer would be enjoyable for new players. But only big balance issues will be fixed by default, others will come as optional options on game start.
Gameplay won't match SMAC's 100%, there may be subtle differences, but the goal is to preserve the overall feel. All rules like units, buildings and technologies will stay the same, AI will be different (hopefully - better), probes fixed (infiltration will last for limited time, probes won't be able to use armor, no foil and cruiser probes). Also, for example, there was a bug with you could select Formers, then press (if I remember correctly) Ctrl+Shift+S and it would build farm + solar collector + road on volcano (while farms aren't allowed there). Such bugs will be fixed too.
Then in v2.0 more crazy features will come, maybe they'll be implemented as mods because it's easier.
But there will always be option 'Force classic mode' that will disable all extras that were not in original game.
For now I added small label to right top corner of main menu, should be clear enough that it's not original SMAC now
Just added planet/moon effects to main menu as in original SMAC