Aside from better graphical effects (ability to zoom, bloom effects, HDR, weather effects), I don't think the interface of Syndicate needs much more work; it is as intuitive now as it was back then. Obviously we'd also have better physics (destructible buildings, etc) and improved AI (pathfinding, NPC intelligence, etc). What I think could really be enhanced is the customisation aspect of the game.
Syndicate was brilliant in that you could research new technologies (with new discoveries in the field speeding up your research path); these technologies were either new weapons or upgrades for your cyborg agents. This was all well and good but eventually you'd have nowhere else to go and customisation stopped outside of the ability to equip your agents for specific missions. What I'd like to see is the ability to research different technologies (bio weapons, stealth, WMD, etc). Within these broad categories the game should allow you to them create your 'own' weapons configurations, for example trip mines that release nerve gas, trip mines that release paralysis gas, trip mines that set off a large explosion of napalm, etc. Instead of plain rocket launchers (GUASS GUN!) you could fire different projectiles (different gases, napalm, etc); instead of flame throwrs you could have short range gas propellants (nerve gas, persuasion gas, whatever). The point is that you should be able to develop the 'base' techologies and then start to create your own combinations of them (having say a primary and secondary fire ability).
Instead of just high-level control over 'taxes' you should be able to manage your territories on a lower level. For example, you should be able to set how your police force acts (Brutal or passive), how your citizens live (poverty or luxury), how much propaganda is forced upon your citizens (very little, extreme) and how much choice people have (full freedom, facist regieme). Some of these would cost money (eg: lifestyle), some could cost you money (choice options) but all would ultimatley affect how your cities work. You could choose to create an air of happiness wherein your citizens are treated well and have a full life choice or you could be totally oppressive and ensure that people are brainwashed on a regular basis).
Why? The reason is simple and obvious; it will let you play the game in the way you want. Not just play the game, but run your company. The overal goal in Syndicate was to rule the world with your corporation; the goal would be the same here but the emphasis would shift away from just ploughing through the missions with guns and winning. The choices you make would directly affect the way the world works around you and the way you play the game.
An example; imagine you were trying to make a move into a territory wherein the current populous were overjoyed with their current government. Your mission was to assassinate the current governor and take over the territory. You'd have to a) go in with all guns blazing, b) sneak around and try and blend in with the population to acheive your goal or c) not acheive the mission, but employ some persuasion and/or propaganda technology to weaken the grip on the current city. Option c) would not be a failure, you just wouldn't take control at that time but it would potentially open up the city for an attempt later on. Option a) could prove unsuccessful as the populous would actively stand up against your insurgence unless you took extreme measures (eg: genocide). Option b would require covert technologies and a specific strategy, perhaps you'd spend one 'mission' scoping out the city and them coming back more prepared. The way you attempt each mission would have an effect on how the population saw your company; if you chose to murder everyone in your way the people of the city would hate you and you'd have a very low popularity rating when you're in control (perhaps meaning rebellions and open doors for insurgent attacks). If you chose to undermine the popularity of the governor, people would be more responsive of you in the future - potentially you'd be seen as a 'liberator' and be welcomed.
It is THIS sort of element that Syndicate should be updated with. The game would then be completely open to new ideas of players - you'd be in the hotseat.
What do you think?