I don't really want another Deus Ex. I'd love more games that are like Deus Ex, as in a shooter/RPG hybrid allowing for a wide variety of paths and playstyles, all wrapped in a dreary cyberpunk package. However, I think the Deus Ex storyline has been finished. Human Revolution shows us how it all starts, and Invisible War shows us how it all ends. I think a new universe, and a new technology to explore, is in order.
What I want in terms of gameplay is a little more RPG. The augmentations are mostly fun and useful, but it's way too easy to max out most of the best ones. I want the upgrade screen to determine my playstyle a little more. The difference between the pacifist and the sadist was only a few augs.
I think the weapons were done almost perfectly. In the beginning, they're all fairly effective at their base stats, so you get to try out a few, but as the game progresses and more upgrades get thrown your way, you're forced to focus on a specific set of weapons or else they all become worthless. And the mods were quite fun (exploding rounds, anyone?). Just make more of the weapons a valid choice, such as the machine pistol, which never really amounts to anything.
Less backtracking through hubs. Walking around Detroit and Lower Hengsha twice each gets tiresome. It would also be cool if the hubs weren't split up into multiple chunks, but I'm not sure how viable that is from a technological standpoint.
Though I'm sure Eidos has learned this lesson at this point, I feel the need to repeat it: don't outsource the bossfights. You've proven, with The Missing Link, that you can make a good boss fight, so just do it yourself next time.
The gold and black color palette, while awesome in its uniqueness and symbolic value, is an idea that needs revision. The same color palette for the whole game really grated on me. Perhaps apply different color palettes to each hub depending on that place's specific issues, with one or more that permeate the entire game to represent the overarching conflict?