Better AI for what is touching strategic moves and bases development/spreading, as the AI is very bad at it in SMAC/SMAX.
For the diplomacy AI, for me, it is already perfect as it is in SMAC/SMAX, as unlike every other Civ-like, i feel my AI opponents to have really their own character and agenda, and usually their decisions are very logic and human-like. I always, and continue to enjoy diplomacy exchanges with the AI in SMAX.
Graphics are very secondary for me, as i enjoy them in their currently 2D with few colors format in SMAC/SMAX, so as long as the certain graphic upgrade does not force a NASA computer upgrade, no need to change drastically what is working very well, i don't need civ4-like 3D while the game plays perfectly in 2D.
I would appreciate even more factions (despite there are already lots of them in the game+expansion), but only under the conditions they are all as well wrote as the ones found in the original game, with their interesting character ingame and their backstory. And no limit to only 7 factions in the same game, i would really like to play with the 14 factions in a same game.
More random events should be a must, as it is a very nice features of those kind of games, making each time you play a bit different, on top of the "just one more turn.." style of gameplay.
More different choices in the workshop affecting the gameplay by offering different style of play, as basically i always feel forced to just use all the best components i have to build my current units if i want to resist/crush the neighbourgh, the workshop while being a nice touch could have been much more in the current game in my opinion. By having not just better, but differently working component, it should introduce more gameplay variation.
More customisation options for generating the rule/game/Planet/factions, should give even more replayability to the user. When it comes to customisation "more is always better".