Step 1: Build the Structure

Download the ivysaur papercraft from pokemonpapercraft.net, which will form the base. It works well, as it has a large, straight-ish back to put the plant in.

Print it out on thicker than normal paper (if available) as that will increase the stability of the design. Make sure your printer can use it. Assemble with glue (and tape, if required).

We used A4 for printing, which resulted in an Ivysaur of 11cm x 10cm.

Step 2: Cover With Paper Mache

In order to make a structurally sound Pokémon, we'll use paper mache to cover the whole body.

Wait till each layer has dried before applying the next one to prevent the papercraft from getting too soggy.

We applied about 4 layers of newspaper and finished off with a layer of white paper for easier painting. Wait at least a day to allow everything to dry through properly.

Step 3: Color

Color your Pokémon using opaque colors (we opted for acrylic paint).

We used light blue as a base and mixed in some green.

In retrospect it might have been cleverer to cut the hole for the pot (next step) before coloring, so you might want to consider doing that first.

Step 4: Cutting a Hole for the Pot

Using a utility knife / X-Acto blade make a hole in the back of the model.

Keep enlarging the hole and testing with the flower pot to get a snug fit.

Step 5: Add Details

Add some character by painting on details:

Eyes
We printed the papercraft again and cut out the eyes to get an idea of their correct size and position. Then painted first a layer of white acrylic paint, then a layer of red and added the pupils using a marker. Also use the marker to draw a line around the eyes to highlight them and give a neater look.

Spots
We simply used green to paint the spots by freehand. They have 3 or more corners, rounded edges and are usually accompanied by a smaller spot next to them.

Teeth
Cut out and glued together from the papercraft (little pyramids) and glued in place.

Nose, ears, toes, eyebrows
Just painted on with acrylic and marker.

Step 6: Finishing Touches

In order to make the Pokémon shiny, we'll use spray lacquer (from the hardware store).

Follow the instructions and coat the model with a few layers of lacquer (we did about 4).

In order to stop water flowing into the body (in case of overwatering the plant) we built a flexible coaster out of aluminium foil and tape and put it inside the body. It needs to be flexible in order to fit through the hole while being larger than the base of the flower pot.

We added some stones in the front to offset the weight of the plant and keep Ivysaur from tipping over.

You are done! Enjoy your shiny Pokémon flower pot.

EDIT:
It seems this instructable has garnered a bit of attention. Here are some articles written on the subject, containing other cool ideas:

EDIT2:

I love the different derivations and improvements that were made to this design. Check out the following projects: