The Oddities of English

I was pondering the strangeness of the English language two days ago, especially how prefixes don't always work according to the expected rule.
For example, the prefix "in-" (meaning not) behaves quite strangely. "Edible" and "inedible" obey the rule and are antonyms. But "flammable" and "inflammable" are not opposites. "Flammable" means able to be set on fire, and "inflammable" means able to be inflamed (i.e. set of fire). Likewise, "habit" and "inhabit" are not opposites the way the rule would suggest. In fact, the relationship is quite complex, considering that "habit" is a noun and "inhabit" is a verb. The relationship between "tense" and "intense" is also not an antonym relationship.
As near as I can tell, the reason for this unusual behavior stems from the etymology of words. Sometimes, the "in-" as a prefix is the result of the Latin "intensifier prefix" (i.e. a prefix meaning "very"). In other words, "inflammable" results from taking "flammable" and adding "very" to the front of it.
This explanation, of course, is limited, and there are no doubt plenty of good etymologists out there who would take me to task for my incomplete ("not complete" :-) ) description of the issue. Still, it is one of the more difficult aspects of English for many speakers, native and non-native. The only aspect that I can think of that is more challenging is the use of the word "up," but that it is a discussion for another day.