Remember earlier when I said that Shadow of Chernobyl is a pile of crap and Call of Pripyat is awesome with an awesome glaze and some nice candles on top? Well I stand by that, but...
In terms of, what for lack of a better word, I will call technology, Cataclysm is leagues better than vanilla or BC. By technology I mean the tools that the devs have and use: phasing, looking for group tool, even achievements, have added to the potential story-telling or game-play potential. Boss mechanics are more interesting and complex, for better or worse. Spells can do a lot more. All sorts of bits are better.
Cataclysm is a better game. But is it really an expansion? Players frequently claim that WoW expansions aren't really expansions, just sequels. They mean that they don't expand our content options, but merely move us onto a new set of content. This is literally false, since expansions until LK haven't actually removed any content, but since WoW is based on progression and the expansions let us leapfrog the content late in the earlier cap, in a practical sense they are replacing them. In this context the earlier content is like Warcraft II; sure we can still fire up a game, but all our friends are playing Warcraft III, or in my case, my friends are playing EVE and City of Villains (no one is perfect), but that's beside the point.
So fine, let's call the expansions sequels. Are they even sequels? Let's rewind.
I have a confession to make: I sometimes make a claim out of ignorance. Usually this is based on an unknown unknown, things which I didn't even know I didn't know. In the case of SoC, I realized that the combat system, perhaps due to a popular mod, is not as bad as I thought, but I am certain of this: a crappy AK is not a good way to evaluate the aiming system of a game, since it can't hit anything anyway. Now I have better guns, with scopes (!), and I can reliably hit my targets, even at moderately long ranges, without needing to 'cheat' by using the crosshairs.
Still, I maintain that CoP is a better game than SoC. Being able to sell weapons or ammo to other stalkers is an improvement. Navigating dialogue with number keys: improvement. Upgrading weapons rather than hoping to stumble across an upgraded version in the middle of nowhere: improvement. Reducing the number of loading screen-separated zones from a dozen or so to three (minus a one-time area): improvement. Assigning hotkeys to inventory items rather than trying to dig through my bags for a first aid kit while someone is shooting at me: improvement. Though that last one is debatable, since it sure makes things more interesting when fights frequently feature thoughts like, "oh shit bleeding, red, oh god I'm dead in about two seconds, where is the first aid... got it! Click, no not drop, use use! Okay I'm alive, good. Now where did that guy sneak off to while I was panicing?" Bang. "Behind me, got it."
On the other hand, as I've played through both, I'm not sure I can call CoP a sequel. Sure, it takes place in the same universe and it is chronologically after SoC, but the feel of the game is a bit different, and I'm not even referring to the mechanics. SoC is based on two goals: figure out who you are and get to Chernobyl. CoP doesn't go anywhere near Chernobyl. The character in CoP has an entirely different background and goal, being utterly alien to the first. Obviously it would be lame if CoP was a repeat: go to Chernobyl and marvel at the improved mechanics and graphics. But for most of the game CoP is like a tangent, feeling as if the stories are almost entirely unrelated.
Beside this there is a major atmospheric shift. I'm easily frightened, so going underground in CoP would make me nervous and jittery. SoC made it looks like a well-lit wonderland, because dammit, it's fucking dark! In CoP I developed a major fear of a mutant called a Burer and had a minor fear of Bloodsuckers, while Snorks just made me want to huddle in a corner. In contrast, in SoC Bloodsuckers are sorta sad to mow down with ease, there are no burers, and snorks remain the only enemy that really scares me. But the environment... It's darker, it's more cramped, it's louder, with shit clanking all over and what the hell was that sound why is there something crashing around in what is supposed to be an abandoned lab? Even outside was eerier.
In short form, Call of Pripat is definitely a fun game, but in terms of atmosphere and story, I'd barely call it a Stalker game, if we're saying that Shadow of Chernobyl defined the series. No comment on Clear Sky because I haven't played it.
I've seen a similar pattern in WoW. Burning Crusade dramatically changed the atmosphere of WoW. Necessary? Probably. Vanilla had a lot of dark undead places and burning orc and dragon places in the late game. Burning Crusade couldn't just add more of the same, so we had purple crystals, divine windchimes, and demons with green technology, by which I mean the technology turned stuff into a hellish evil green, which sorta makes Al Gore look bad. Wrath of the Lich King brought back undead, but added a twist: cold. Then Cataclysm switched it all over the place and made an entire zone based on scaring people who are afraid of water.
As for the stories, it's been similarly all over the place. The Scourge was left damaged, but nowhere near destroyed when we went off to Outland. Then we all got in ships and went to fight the Scourge. Problem solved! World blows up. In actuality LK and Cataclsym returned to old stories from vanilla: the Scourge and Twilight's Hammer (Old God cultists), respectively, but how long ago was that? Long ago. Returning to the central theme can still seem tangential if you've been away from it for long enough.
Of course this is highly subjective. For one person the mechanical improvements can seem like dramatic gameplay changes, while another player may see major changes as relatively minor and inconsequential in the overall theme or style of the game. Have you run across similar examples where a sequel, or expansion, so dramatically changed a game that it is barely recognizable as being from the same company in the same universe?
As a parting example: Knights of the Old Republic was awesome, however while Pazaak (same general idea as Blackjack, but with the skill-luck mix tipped more toward skill) was a neat game, the hardwired cheating by the computer (it always went second) made it a lot less fun than it could have been. Knights of the Old Republic II had a much improved Pazaak game (alternating starts!), but at times seemed slightly off, as if it were somehow unfinished or rushed. Big surprise, it was. So let's end with some appreciation of Blizzard's slow-as-frozen-molasses development speed.