Imagine that there was a language 2000-2500 years ago (and even earlier, if we take Homer), that had a very precise structure and could phrase ideas in a very precise manner (pretty much like German), long and short vowels and a system that helped you read it properly using the appropriate stress marks and breathings (that was introduced in the Hellenistic years when Greek was like today's English, a lingua franca).

Fast forward 2500 years. The structure is much simpler, but the links to the old form are not broken totally. Only obfuscated. Many words of the current form include words from the Balkan area, Turkey, Italy and France. So etymology can't help always, unless if you're interested into gathering facts from other languages too.

Also, the only stress mark left (acute, see: https://en.wikipedia.org/wiki/Diacritic) doesn't help that much to get a perfect pronunciation only by reading. Also, even if the letters look different, there are groups of letters and diphthongs that are pronounced the same. Examples: (o, ω), (η, ι, οι, ει), (ε, αι).

So, to learn how to read it properly, you have to live in Greece for some time, or to hang around with Greeks. And to write it properly, you have to take classes or/and read some Greek literature and poetry. And even then, the way some words are written has changed over time and I suppose it will keep changing. Examples: (τρένο, τραίνο) and (ταξείδι, ταξίδι).

It's pretty much like nature. To answer to all the why's, you have to go really deep, or else you'll have to memorize lots of facts from everyday experience. Also the problem of diglossia hasn't been solved properly, which fucked up even more the language according to Babiniotis (https://en.wikipedia.org/wiki/Georgios_Babiniotis).

So there you have it. A very old structured and precise language, that has evolved into a simpler, more flexible and much more intuitive language.

PS: using a new alphabet is a first barrier one has to overcome too. It pretty much scrambles your brain.