The reasons are mostly historic. For instance... The verb "Aller" comes from 3 differents latin verbs who merged... Vadere (je vais, tu vas...) Allare (nous allons) Ire (j'irai, tu iras...) The verb "être" comes from two latins verbs who are still different in Spanish : ser (je serai) estar (vous êtes, j'étais...)

The short answer is just accept them. French evolved from Latin over a period of roughly 2000 years and certain oddities of French are a result of historical changes. The long answer is take a historical linguistics univeristy course and spend 200 hours to learn how Latin evolved into Romance which evolved into old French which evolved in modern French.

Actually, I have no answer to your question, even though I lived in France for 20 years. But I do know that the French people are very proud of their culture and language. Maybe they made all these complicated verb conjugations to keep their language very special and difficult to learn, so that only the very best students would be able to achieve this goal. Or perhaps it's a way of making sure that all those teachers of French have plenty of work for years and years, as they struggle to teach their students the complexities of this language!! ;-)

The issue with this type of words is that it was decided to be that way by convention. But if the "n" in "prennent" was not doubled, it would be spelled as "prènent" to suit the pronunciation. Now I think, the French academy decided to do it that way maybe to compensate the loss of "d".

I'm not sure there's a hard and fast answer for irregular verbs. The problem with language is it's spoken by people. Sometimes people are lazy and change things. Sometimes it's to avoid confusion. A good French example of this is aujourd'hui, which literally means "the day today," because hui also meant something else and people got confused. But I think that underlying it all there are unwritten rules about the way words are spoken. A Chinese man can have a good chance at reading an unfamiliar character because there are clues in characters and he understands how a Chinese person speaks. I think a French person saying "Ils prennent," says it because it just feels like French to him. We on the outside try to learn the rules of grammar for our chosen language, but really we're all trying to get to the place where we speak by instinct, not by rules. The wonderful news is we can. The more "comprehensible input" your brain gets, the more it will make up its own unwritten rules about what is French and what isn't, until one day when it will all just feel right. I'm sorry there's no easy answer, but stay positive and expose yourself to a wide variety of French. It will all work out well.