Serious Sam: The Second Encounter was actually surprisingly different too. It had much more open and non-linear level design, and while it arguably wasn't really "better" it was certainly a different take on things. I don't think Serious Sam 2 is that bad, I think a lot of people mostly dislike the art style changes, while Serious Sam 3 is mostly a return to form after the first few levels (but it takes about 1/3 the game to truly get there again). The series has had ups and downs and most of it seems to be a result of the developer trying to mix up the formula rather than churn the same game out over again - it worked in The Second Encounter, but if it hadn't, would we still be looking at Serious Sam so fondly, I wonder?
The Second Encounter was what I call a "straight-up" sequel, which is when the development time is only a year or so. A year gives the developers time to learn from their mistakes, look at what fans and reviewers said and act on it where needed, and add only minimal new content but all without straying too far from the established formula. Some of the best sequels ever made were done in this way. Eye of the Beholder 2, Doom 2, Fallout 2, just to name some examples. I consider SE to be the best Serious Sam game out there, it's challenging, varied, interesting level design and just about the right length, even though the final level can be VERY draining.
Now, as for Serious Sam 2... I don't mind the art style changes that much. It's everything else. The levels are MUCH smaller than in any other Serious Sam game (excluding perhaps the Next Encounter, a console-only title I've yet had a chance to play) and there are invisible walls all over the place as well. Serious Sam FE and SE were praised for their freedom of movement, you could walk out into the desert in FE, you could easily be thrown out of the level boundaries on one early level in SE (so easily in fact that there are bounders all around the map to get you back into the action) but in SSam 2 you'll run into the level boundaries almost smack-on. Only the medieval level has really large areas.
The weapons are... pathetic. All of them. There's a rotary shotgun that's just as effective at point-blank range and picking off distant targets. The Minigun feels like it's nibbling at your ammo instead of chewing through it. They all just feel wrong.
The enemies are just as pathetic. Most of them die if you as much as glance at them. What's worse, while SSam2 claims to have dozens of enemy types, the truth is much worse. There are certain "archetypes" of enemies, and then there are versions of those archetypes for each world. Kamikaze bombers become bomb-wielding clowns on unicycles in the Oriental World, for example. Melee enemies, weak cannon fodder, fast-moving medium troops, big mothas, etc. All have several vareties of them, none of them feel unique in any way.
The humour and cuteness is over the top. SSam has always has humour, but this feels like Serious Kitty: The Greeting. That NETRISCA now talks, and NEVER seems to shut up, is also a downpoint. Do I have to mention the "EXTRA LIIIIIFFE!" sound to make people twitch in horror?
The new vehicles sounded interesting, but the fun was lost for me when I realized that none of the cool tire-based vehicles that were shown in the tech demos made the cut.
SSam 2 is a huge departure from what makes the SSam games stand out. It does explain somewhat why 4 years passed between SSam 2 and another SSam game was released (which turned out to be the HD releases of FE and SE) and another 2 more years until a new title was released (SSam 3).
EDIT: Typo, meant SE, not FE.