X- is pronounced like sh
Q- is pronounced like ch
C- is pronounced like ts
-iu is pronounced like yo
-ian is pronounced like yen
etc
In this regard even Wade-Giles does a better job in my opinion.
Yo be clear, mandarin is of the most concern, just want to raise the issue that while true, it's not uniform throughout the language.
For native users of pinyin, the consistency with English pronunciation is essentially irrelevant.
A brief example, yes/is, approx [shi], might be pronounced approx [si], etc. But it's mandarin and not hakka, min, etc.
Kazakh makes a phonemic distinction between [g] and [ɣ]. Slovene, and most European languages, doesn’t have that distinction and their writing systems are therefore not equipped to represent it.
In any event, as per English, French, among others, an alphabet does not have to orthographically represent the phonemes exactly.
The way it's been proposed reminds me of the old Wade-Giles custom of adding apostrophes, breves and other diacritical marks. Pinyin is so much cleaner (except a few umlauts).