Actually, I had no problems with the controls. They were intuitive for the most part, and behaved well. The character movement was sort of stiff, but it's too be expected in a game of that sort.
My main problem was the unvaried gameplay and the atrocious level design. It would sometimes take me hours to pass a level. Not because of enemies. Not because of mission objectives. Not because of being seen. But because I couldn't find the single blasted beam, ladder, or path that I was supposed to take to get out of the dark-ass section of the level that I was stuck in and couldn't find my way out of. Difficult enemies or situations is fine. Difficult level design is not.
The other big problem I had with the game is the general inability of the game to draw a person in. Metal Gear Solid always had a joke of some kind to keep things light. Splinter Cell had none of that. That's good, as it showed the developers tried to distinguish themselves from Konami. What's bad is that it just felt like a missing feature. The game wasn't really fun or rewarding at all. I finished a level to find another boring section of poorly told story, and another level that features objectives that are perfectly accomplishable, providing you can figure out exactly what it is that you are supposed to do to get there.
Writing these two points in detail has brought to mind two more points that I must dig into now...
Everything in the game just felt scripted. You knew when you were supposed to use certain weapons. You knew when you were supposed to wall jump. You knew when you were supposed to rappel through a window. This wouldn't be a problem, except that those were often the ONLY actions that would accomplish the mission for you. The developers forgot one of the cornerstones of good game design when thinking up those scenarios. You are supposed to make each puzzle solvable in a variety of methods. If there's a ravine that you can't cross, then you should be able to find a boat, or use a zip cord to get across. SOMETHING to that effect. Oftentimes, you had to keep trying until you found the solution the developer intended.
The last thing that really bothered me about the game was how I could leave a dead body lying in a corner of a freezer and somebody would find the body a minute later, while if I left the body laying in a dark hallway, nobody would think anything of it. Metal Gear Solid 2 is a game that I don't really like that much, but at least the rules regarding bodies lying in the middle of a hallway were FAIR. If you left a body lying in the corner of a freezer in that game, nobody would likely notice, because the game would take the time to figure out whether any guards are likely to patrol that area or not.