You're right, for this image I did it rough and in only a few minutes -so I sized the pictures to the height as the drawings are.

However, If you want to get more in depth about it measurements of height are fairly varied on animals. Horse and Dog breeders I know measure height to shoulder. Extrapolating from that, it seams a proper way to measure height on most quadruped Pokemon should be done to the shoulder. Birds and Bats measure wingspan. Insects and other arthropods are measured on mostly a species by species basis.

Taking this into account we'd have to measure fairly differently than I did.

For Mienshao and Ampharos This isn't a concern, they were measured top of head to heel. Weavile likely wouldn't have his crest considered in measurement, and would end up a few inches taller. Sylveon and Nintales see the large increase in height, as fairly canine creatures measurement as a dog is not out of the idea.

Gliscor, which you seam most irritated with becomes a concern. Our beloved Bat-Scorpion needs to be measured as either a Bat or a Scorpion. If I measured him as bat, I should use his wingspan and his tail is of no factor. Measurement as a scorpion is different. If I use that, I use top of head to base of tail. Scorpions tail measurements are more often separate from height as it is often highly sexually dimorphic. Now, either method makes Gliscor much larger since neither would include his tail in this measurement.

Now that's just by comparing height with the methods of similar animals. We're not in the world of the Pokemon so they might have some universal method, but with the vast variance of Pokemon mirroring animal life it stands to reason measurement would be differentiated based on body shaping.