1. Pokemon Intelligence
The measure of a pokemon's intelligence is dependent on a number of factors. Translating these into game mechanics, they would roughly be Level, IVs, and Identity.
At extremely low levels – that is to say, when very young – pokemon are, for the most part, quite unintelligent. As they mature – and note, this is not solely a factor of age, but also of experience – their capacity for higher thought increases.
The base value, on the other hand, is an inherent value. In-game, each pokemon has a range of stat values that are possible, depending on the Individual Values, generated when you first encounter the pokemon.
This translates fairly well – it is entirely possible to find a very young pokemon that is more than just a mindless ball of hormones and instincts, but it is rather unlikely. As the pokemon mature, this difference becomes more pronounced, as the multiplier starts to do its work. Equally, however, it is possible to find pokemon that are inherently unintelligent – and even if they live an old age, they will not become all that much more intelligent.
This brings to light one of the major roles of Breeders in the pokemon world. If you have two parents that are in a high intelligence bracket, it is significantly more likely that any offspring will be of a high inherent intelligence themselves.
In addition to these is the actual species of pokemon. A psychic pokemon such as Abra or Ralts will have a higher capacity for intelligence than a more common pokemon such as Rattata. Generally, a high rarity is a decent indicator of high intelligence, though it isn't always the case.
The result of all of this? That tiny level 2 Pidgey that attacked you the moment you left your home town is more than likely just an animal defending its nest. Lance's level 60 Dragonite, though, is at least as intelligent as he is – probably more so.
And this leads to my second chapter: 2. Pokemon Societies.