I would definately second that it is because it started as a collection of house rules to handle dungeon crawls. There was never any real coherent design behind the original setup. For example, the magic system is entirely seperate from the combat system. The skill system is bolted on seperately again, and hacked together at best. The concepts are not properly defined, giving you such results as power attacks being less likely to get through armour, and elephants being some of the best animals at dodging things. There is also an abundance of absolute effects with specific defenses, and very rarely is there trade offs. For example, there is no "obscure vision" spell line applying scaling penalties, there is simply "blindness". Iron heart surge like effects are much needed to avoid christmas trees of items against every shut down effect. Ideally there should be some cost to the defender that depends on the power of the effect, but the system is not set up to facilitate that. By the time you get past level 10 the system is a mess.

Special mention goes to black tentacles, which creates magically invincible nonmagical tentacles that hit even if a god gives you an AC of 'no' (+100 sacred bonus), then grapple without following the grapple rules... Why!?

Basically the system was built outwards from wizards on a dungeon crawl without much planning, so the parts don't line up. This gets more extreme the further from 'basic' you get: ie, higher level.