I agree about STALKER: Clear Sky's ending, as the first game too, it was a letdown after so many great non-pitched battles in varied terrain before.
Clear Sky had some great things though - the swamps are excellent, red forest was excellent - both new areas. The finding anomalies is much improved and more unpredictable. You get mini-faction missions were are okay, adding more on top of the rather boring ones you got in the original from factions.
Faction wars - not terrible, although I didn't do much in them. It basically amounted to nothing (no faction could be wiped out sadly, and it all basically takes place in one big area). If it was more varied, more random, and allowed total vanquish or at least defeat to a "home area" it'd have been much more fun - basically because I'd not have needed to keep killing the same bandits over and over and over... however, it did add much in the way of life to the zone. The wars were part of it (like the original, only here more pronounced). Only real problem with the fights is the "insane grenade usage" - get too close and you die, die die die.
Also, it has upgrading and repairing weapons - very much customising them how you like for tons o' cash. Makes it much more enjoyable (yes, however I did up the weight limit, I still think it's tiny).
Nice prequel though.
The first game had by far more enjoyable progression - the journey was just a great over-arching part of visiting tons of people and places (and monsters). Longer of course. With mods I played with, much fun too, especially since it had it modded for some better AI.
The main bit I remember is fighting the balls 'o light once I figured out they were the gits hurling things at me - and the boss in that lab too. The hunters as well, the invisible creeps, were pretty intense. With the mod's AI they did actually become pretty rogue and epic (clear sky for some reason cordoned them off into zones, so it was really strange how they ran around in circles not being able to get to you sometimes...).
It's a great set of RPG/FPS games for sure. AI I think really is the main part that is enjoyable. Wild dogs, fights in open terrain and underground, squads and cover usage - as well as lots of non-combat stuff they do, is pretty great to just immerse yourself in. The story is okay (once you know the details) but it's more about the world then the rather silly things you have to do and half-baked ending. The actual world is very deep, lots of story shown through gameplay and playing not reading things or listening to stories.
The only major thing I disliked, and this is a tiny part, is the role of the army. I know generic bad guys are needed, but I actually really enjoy the fact there are outsiders still patrolling and going into the zone, and yet you have to kill them over and over. This third one, I think (?) you take part in an undercover op for them, which is great. I think they have a ton of story potential since they're outsiders, for better or worse. After all, since the player is essentially always cast as an outsider...
I hope to see great things from STALKER 2 - meant to be in the Crysis engine or something? Continuous areas would be cool

the views would be epic, the fights even better, even if they can't replicate the unique AI (although I hope they try their hardest to!).