Well, I'm Thai and I support your idea that Thai has very difficult writing system. But, the reason is much beyond that. other than the 5 tone (4 symbol to locate the tone), 3 group of vocal alphabet (high, med, and low) and the vowel that goes ways round the character, we also have the multiple final consonant which make things more complicated.
ใครขายไข่ไก่ "khrai khái khài kài" (literally means who sell chicken egg) this might sound crazy for foreigner. this sentence has not yet to do with final consonant. but the short and long sound vowel and the tone make it difficult. noted that ก(k) is not same with ข and ค(kh). and ข and ค is same sound but differ in tone.