There are a few reasons that pop to my mind, actually:
1 - Pokedex Completion
Certain Pokemon can not be obtained without trading, so this makes it easier for trainers to encounter them. Good Guy GameFreak decided to help all the trainers out there (specially Generation 1 and 2, where trading was not as evolved and commonplace as it is now).
2- Intimidation
Directly quoting Lucas, who has come all the way from Sinnoh (lulz ), having a Pokemon of the final stage is essential for Gym Leaders to 'establish dominance'. Not really, but you know, having the final stage shows power and commitment and so on and so forth.
3 - Corollary to ^
However, having under levelled evolution is weird. Why continue, then?
Simply this: Trainers at that part of the game are still too weak to actually defeat the obviously stronger stage 3 Pokemon to win (comfortably) at the correct at which it evolves, and it makes the game so much more harder. Not cool for the 'pros', but remember, a lot of people are beginners.
Solution? Good Guy GameFreak decides to bend the rules to help out all the newbies. Better have them question poor/ wrong levelled evolutions than crib about a game they can't beat (Darks Souls: II, and Takeshi's Challenge have that covered as well), right?
Those are, of course, just my observations. Of course, the actual GameFreak reason might differ.
