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I'm writing a story in English but I'm not a native. I’m a Brazilian Portuguese speaker.

It bothers me how repetitive and ambiguous pronouns can be. In my language we can use the equivalent to ‘this one’ instead of he/she/it etc. It’s less usual, but still sounds natural. But I don’t know how it sounds to a native English speaker. The only examples I found in English were archaic.

Example:

John saw Mario again after three years, and thought that he
(Mario, not John) lost a lot of weight.

Does it sound weird if I write instead:

John saw Mario again after three years, and thought that this one
lost a lot of weight.

I wonder that something like ‘the guy’ could be used instead of ‘Mario’, but it would not sound good if Mario is a well known character by the reader. Of course I can use Mario again, but it doesn't work well in the sentence that concerns me.

There is a distinct use of "this one" in English which is a matter of usage rather than grammar. It is used by one person to refer to another person (often, though not always, an inferior), who has done something stupid. Thus:

"We were driving along in the rain and this one decided to hit the sunroof switch."

or:

"We were all in the living room watching the game when this one decided to put the cat in the microwave."

(This is an idiomatic usage, so it will be far more common in some parts of the English speaking world than others.)

Your example does not quite fit this idiomatic usage pattern, but it is close enough to it that someone accustomed to that usage might assume that you intended to use that idiom and got it wrong. (That was the first thing I thought of when I read it.)

In any case, your formulation just is not common or idiomatic usage in English, so the short answer to your question is, no.

What you could do to introduce variety into your example question is something like this:

John saw Mario again after three years, and thought that his friend had lost a lot of weight.