There's a glossary section that highlights the rough gradation of the sizes (it's rough in that there are some cards that could fit into two values) - http://phylogame.org/glossary/ If a number seems off, the best thing to do is leave a comment in the permalink for the card.
For the terrain, we had to simplify and sort of narrow down to 7 approximate types of landscape (out of the huge number of different terrains we could of listed). Again, there's a little bit of gray here. For example, moorlands and mountains tend to be somewhere between grassland and tundra type scenarios, where the difference would depend on the level of vegetation (or in the case of mountains, how high up you go). I'd say farmland best fits under the grassland category, although an orchard could be thought of more closely as a forest type.
Food chain value of 4 is pretty rare, and usually reserved for organisms that are clearly apex predators hunting large prey. i.e.For the UK, I'm not sure there really would be something comparable to, say, a lion or a polar bear. i.e. for a fox, it still works as a three because a 3 can eat a 3 if the scale works. Still, I see the issue (i.e. why can't a lion eat a massive #2?) Hmm... maybe we need to get rid of 4s or be more careful with them (i.e. I think the Polar bear still works, as well as something like a killer whale).
The move and flight numbers are pretty arbitrary (with the exception of creatures who are particularly noted for their speed or distance). 2 was a value chosen, because it work in the context of allowing players to "escape" from detrimental situations, without it being too easy to escape. It's one of those numbers that primarily came to be by play testing.
Hope this helps!
(Also, we just released a new starter deck and have slightly modified the rules a bit - go to http://phylogame.org and click on the links just after the START)