Geodude/Graveler/Golem:
Now at first you would consider Geodude just a rock with a face, but the thing that I think elevates Geodude is the addition of the arms. The human-like arms made of rock helps Geodude stand out amongst rocks and you can see how it can fight aside from ramming into its opponent.
Graveler can be seen as an evolution of that concept. The rock has grown bigger and so it has also grew a pair of legs and another set of arms. Also the rock has molded eyebrows on it, accentuating Graveler's face while still being part of the rock body.
If anything I'd argue Golem was the boring looking one (and now thinking about it doesn't really fit with Geodude and Graveler, not in concept or color but that's another issue). Golem is pretty much a lizard head, arms, and legs attached to a cobbled together boulder. Now by itself it looks fine, its unique looking as you wonder whats inside that boulder body which I would say visually looks more interesting being cobbled together instead of just another giant rock.
Magnemite/Magneton/Magnezone:
While people say Magnemite is the magnet Pokemon, as you can see there's more to it then being a magnet with an eyeball. If anything its a magnet, metal ball, and screw Pokemon, it actually has more screws then magnets (though the magnets of course are the most visible). It actually looks like a robot based around a theme of magnets than a plain magnet.
Magneton... is just three Magnemites, so I guess take what I said about Magnemite and read it three more times or something. Actually, Magneton has less magnets then 3 Magnemites, for some reason the bottom two Magnemites lost one of their feet screws (the bottom two Magnemite are actually upside down).
As for Magnezone, its actually a magnet combined with a UFO, changing up the design (though keeping the multi-body design as well, except now the "lesser" Magnemites have simply become shoulder pieces, but at least they keep their head screw while the main Magnemite gets it replaced by an antenna). It not only looks more like a robot, it looks like a robot from another planet. They even manage to change up the main Magnemite's eye by giving it a giant red pupil, the better to search out for puny humans to abduct.
Grimer/Muk:
How can a pile of sludge not be a lazy design, let alone two? Well Grimer is an example of simplicity at work. Yes, its a pile of sludge with a face. The pile of sludge has been formed into a vague face and two hands, but its still a pile of sludge. And guess what, that's what Grimer only ever tries to be. It's a toxic sludge monster with over-lapping layers of various shades of purple sludge. It gives it a simplistic personality, thus when it shows off any kind of personality which it can do with it having not only a face but hands it makes the design work even better.
Okay, but isn't Muk the same thing? Yes, but in a different way. While Grimer is able to "stand upright", Muk has completely collapsed under its own weight. It looks like the only thing that's protruding out is the top of its head or gives it a hunchback appearance. Its arms and hands are also less define then when it was a Grimer, it having to spread them out to even look like individual fingers. Finally its face has also gotten so huge that it can't completely open its mouth without their being a streak of slime connecting the bottom and top. It's pretty much what you would expect to happen to Grimer upon becoming a bigger pile of sludge, and that's why the design works.
Onix/Steelix:
The first of the hybrid object Pokemon, Onix is a giant snake made of segmented rocks. That said, its still a bit of a dull design but one major factor of Onix's design is also its size. Those aren't pebbles its made from, those are giant boulders with even the rocks making up its tail being the size of your head. Also they added that spike on the top of its head to I guess give its face some additional features, removing does sort of make Onix look like its bald. Actually you can say the horn helps it look like an animal as many animals have head adornments even if they serve no purpose.
Steelix you would think is the same design but it has some differences to make it different but they make it work. The major change is with the head as they decided to put more emphasis on its lower jaw and replacing the head spike with stubby protrusions making its head look more squished, sort of giving it a brutish appearance. Its body is even enhanced with spikes coming out of certain boulders, which gives it an even large appearance. So with Steelix you can say they further emphasized what made Onix's design work on an otherwise simple concept, rock snake.
We're not going to cover Mega Evolutions since they're a whole different beast.
Voltorb/Electrode:
Another simplistic design. Voltorb is just a ball with eyes, nothing more nothing less. You'd think that would qualify for a lazy design, except that the ball its based upon is a Poke Ball, an important device in the Pokemon world. Suddenly Voltorb's design goes from being lazy as one wonders how a creature like this came into existence looking just like one of the world's most important devices... before it blows up in your face. Because that's another part of Voltorb's design that makes it work, its not only a ball (which gives it a high speed stat) but since it has no arms or legs to attack it has also become a bomb.
Electrode both works and doesn't work as an evolution to Voltorb, and that's to the benefit of its design. It turns upside down and grows a mouth, yet its eyes completely change and the mouth is a toothy grin. It goes from being constantly angry to some sort of a wise guy. Where did the teeth come from? Those eyebrows aren't even attached to its face! You know what Electrode is? It's a JOKE to the concept of slapping a face onto an object and calling it a new creature. That's right, its meant to look ridiculous so much so that they played around with its design to give it things that wouldn't make sense for it to have. And that's why its design works, as its pretty much a parody of the concept. Also all it does it still explode so that helps too.
Koffing/Weezing:
Koffing is a combination of a toxic cloud and a mine, giving us this odd floating purple spike ball filled with gas... that has a derpy face on it. Koffing is already an odd design that just adding a face to it wasn't going to make it any less odd, and so they gave it a face that you wouldn't think would be on an otherwise otherworldly looking object. Koffing has a face of someone you think you can have fun with... until you suffocate on the noxious gas it leaks out. And just to further offset the innocent face, lets put a skull and crossbone just below its mouth. Thus we get a floating purple spike ball of poison has who happily shows that he's highly dangerous. Its the offset that helps with the design.
Weezing is what happens when it realizes its an abomination. It mutates into a molecule-looking toxic cloud mine, with one of its new orbs also gaining a equally frowny face. The last orb is just there to stick them together those some Pokedex descriptions says it also becomes a face, probably also sad looking. I think what makes Weezing work is that it looks so depressed, a complete 180 of how its pre-evolution was portrayed being. Koffing was just happy to be alive, but Weezing just wants the suffering to stop. They make a hilariously depressing comedic tragic duo. Coming this fall to a TV near you!
Porygon/Porgyon2/Porygon-Z:
Based on a 3D object, what makes the Porygon family's design work is that it's actually meant to be a progression of advancing technology. Porygon is suppose to look like a blocky bird-like creature, simple in design since early 3D technology was only able to handle making simple objects like that.
Porygon2 shows the advancement of technology, as now the software that could only handle the low-poly Porygon can now handle an object having more polygons, so Porygon's edges are smoothed out making it look rounder giving us Porygon2. Not only that, they're also able to show more physical details such as the beak being a separate part of the face and the tail having different widths, something Porygon couldn't do as it needed to keep things simple such as having the beak be just the tip of the face but colored differently and the tail having to be a be made of straight lines.
Porygon-Z is both an advancement but also an aversion to the idea. It's a poorly modded Porygon-Z which has caused it to glitch out. The neat thing about Porygon-Z is that you can actually take it apart and pretty much put it back together so that it looks like a Porygon 2 (except the eyes would still be bugged out and the bottom blue part wouldn't exactly match). Comparing it to Porygon2, Porygon-Z's head has been flipped upside down making its neck into a horn while the legs and tail have been moves and flipped so that they're going in the direction of the stomach. They pretty much did all they could to make it look like a glitched out Porygon2 which is what I think one of the neatest thing about its design.