I've only played Blood Money, but I have over a hundred hours clocked into it. There are a few things I hope they improve in a sequel:
Better AI. This doesn't just mean combat AI, since if you are playing it well there should be very little combat. I'm talking more about more realistic reactions from people.
An example is the Mardi Gras level on Blood Money You walk into the kitchen of a nightclub. This simple act of trespass is considered worthy of death by the security guards. Why? Reactions should be scaled; trespassing once or twice triggers a warning from the guards, keep doing it and they try to arrest you. Pull a weapon, then lethal force can be used.
Another example from the same level. If you try and go into a building occupied by your target and his bodyguards (rival assassins AKA criminals) and the guards start shooting you, you run outside only for the police to help the guards. The police have no idea whats going on, yet they automatically side with the gun toting chicken people (yes, they're dressed as chickens.)
More varied melee. Yes, you can go up to someone and knee them in the face, but Agent 47 is a trained killer. He must surely have some sort of martial arts training? Splinter Cell Conviction uses some very exciting, brutal melee attacks based on Krav Maga, a martial art devloped by the IDF (one of the few things I liked about Conviction was the melee). Now, the melee system shouldn't be so overpowered that it's a crutch, but being able to walk up to a guard and silently neutralise him, without the ridiculous knee-to-the-face-then-punch-twice. Its stupid to watch and lets the guard cry out in pain. Not very professional.
The third thing I'd like to see would be more varied weapons, and better use for weapons. Blood Money allows you too upgrade a selection of weapons, and keep firearms that you pick up during missions. However, you cannot customise any weapons other than the default. You also cannot keep melee weapons, such as knives, hammers and fire extinguishers. One of the things that gave Blood Money replay value was trying to complete the mission only using a kitchen knife, or the hammer. Unfortunately, you had to choose missions that had these weapons, then find them.
These are just a few things that I found wrong, or at least immersion-breaking. Theres alot more, such as the speed with which you change clothes, or the fact that the clothes are always pristine despite the fact the previous wearer was blown backwards with a shotgun. Those are just a few irritants, whereas those three could extend playtime enormously I think.
