Absence of /kha/, /ga/, /gha/, /cha/, /tha/, etc, signs in T

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That is true, actually Malayalam kha and Malayalam vaa are similar, except Malayalam vaa doesn't have the little circle like kha(or the Tamil vaa). I don't know about dha, that letter resembles the Tamil maa. A lot of letters are definitely borrowed from Tamil, and even some letters are switched around with different pronunciations. You cannot borrow letters from other Dravidian languages, because they don't flow with Thamizh, only suggestion is Malayalam because it definitely resembles Thamizh, and that is about it, unless some letters are made up.
Either way, something needs to be done.
The most beautiful letter in Tamil and Malayalam in my opinion is "ja", I just love the way it is written.