Clear Sky is certainly the weakest but it's by no means a bad game. They're all so similar anyway that you can't really go wrong. Really the biggest problem with Clear Sky is that the faction wars system never really works, but that entirely a side thing after the first zone. Other than that it does many many improvements to the series that are carried into the final game.
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I remember getting bored after around 10 hours of the third. The story goes nowhere, and the characters are very boring. The gunplay is average at best and there's not a whole lot of RPG to be had. After 10 hours I had enough ammo and health items to take down a small army.
But everyone keeps recommending them, so I don't know. I guess I just don't see the appeal.
Wonky and messy as hell, but it's still entirely playable and quite enjoyable. Unlike a lot of other games I would describe as "messy", at least the UI is intuitive and straight forward. They're also pretty difficult games; you're not going to be a super hero at any point.