With the limited experience I have so far, this is what I think Firaxis should focus on. I reserve the right to change my mind later when I know how you're really supposed to play this game.
In order of decending priority...
- Bug fixes
- Balance issues
- User interface improvements
- Setting the standards for a great strategy game SDK
- Expand on great leaders and wonders
- New civ leaders
- Other new game features and content (including new civs, terrain, etc)
Balance
About game balance, they should fix tech pace so getting a tech actually means something in the late game of standard maps. What's fun about tech inflation?
I'm sure there are other balance issues, but I am not experienced enough to confidently list any others just yet. However, balance has to be the first and most important area to focus on.
User interface and game control
A lot of good suggestions have been made in the line of something like this: Give the player more control while eliminating unneccessary micro-management and make important events and information more accessible.
Units
As far as new units, I would actually want to see one taken out - The Explorer. I might be missing something, but I just don't get it. What's the point with this unit really? I feel bad for the animation artist and whoever spent time to make it...
If a new unit should be added to the game it should be because of game balance reasons and in that case I would want to add a Siege Tower unit available maybe sometime between Catapult and Cannon. It would be used to help capture cities a little quicker. I think warfare just takes too long now to the point that it is kind of tedious/not as fun. Possibly war weariness or war cost could be scaled up to counter balance excessive and prolonged warmongering (if that would become an issue).
Promotions
In the line of combat, several of the high level promotions in the promotion tree seem to be rarely used. Maybe I'm just not skilled enough to drill down it (I usually get 4 promotions/unit at the most). But it seems like a waste to have a deep promotion tree if parts of it is barely ever used. It is a core game balance issue though, so I guess changing the exp-cost for promotions might be a can of worms to play test. Promotions are fun though, so adding something here would be great as long as it does not come at the expense of balance.
Great people and Wonders (etc)
Great people are just awsome and something I would like to see expanded on somehow - again, as long as it does not break game balance (hrm, is there an echo in here?

). I really like wonders so seeing some more of that would be great. Building wonders are just fun and also blends well with expanding on great people. For instance, if a new type of great people/person would be added (ie for military/health/happiness/whatever), new wonders would probably be added with it. We might see the Great Wall back for that, who knows.
About other buildings and bonuses/terrain, I think it is similar to units. Adding new buildings to improve game balance only would be the best way to go I think. If a new regular building doesn't improve game play it is content and not as important to me at this point.
Civs and leaders
About leaders, suggesting Stalin and Lenin and not Hitler, etc, is ... well, explainable but kind of rediculous. Heck, why not put in Robert Mugabe, Idi Amin and Pol Pot and all the other butchers of history too? It could add some interesting flavour to diplomacy. Other than that I really don't have much in the line of suggestions here except that it would be nice to see two leaders per civ to give more variations and thus feature the leader traits some more, which I really like. The leaders and their traits really make the civs come alive.
About new civs, it would be fun but it is not as important to me as some of the other things listed above. I regard them as content. The MOD community will take care of adding depth and replayability as long as the SDK is good. New civilizations, new terrain and bonuses, etc are things that have the potential to develop and improve over time.
Other game types
I really don't have any experience with multiplayer games or scenarios so I have no suggestions here. It is not that important to me.
The bottom line
It would be great if Firaxis focused first on what only they can do best, that is build a great core game that has excellent game balance, very few defects and a great SDK.
When they are done with that it would be great if they could also start adding improved game elements and more content. I would gladly pay for that kind of quality expansion, but only in due time.