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I want to write this paragraph in my project proposal:

I have the intention of improving this paper and I want to do this Improve in one of these 3 subjects:
1) modelling
2) simulation
3) ....

I want these text to seem more sophisticated and I have some questions about what I've got so far:
1) Is the word "subject" appropriate here?
2) Can I use "have the intention of..." or it is supposed to use only in the negative form?
3) Can I replace "I want to do this Improve..." with a better phrase

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    I recommend you break this into three questions, with the following in mind: 1) It's difficult to tell if “subject” is more appropriate without more context around how these items are treated in your paper. 2-3) Explain your thoughts on these some more. Provide alternatives that you think might be correct, and write as much as possible about the result you want to end up with. Generally speaking, providing more detail will get you better answers. This goes hand in hand with my request to restrict yourself to one English issue per post. Focus → clarity → quality. – Tyler James Young Feb 21 '14 at 16:47
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    I agree wholeheartedly with TJY's exhortation: Focus → clarity → quality. That said, I don't think this needs to be three separate questions; in my opinion, they are all based on a single sentence, and are interrelated enough that they can be addressed in one ELL question. – J.R. Feb 21 '14 at 17:17
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I'll answer these questions in reverse order:

3) Can I replace "I want to do this Improve..." with a better phrase?

Yes; improve is a verb, not a noun. Therefore, you should say, "I want to do this improvement..."

2) Can I use "have the intention of..." or it is supposed to use only in the negative form?

You can use this, but it's unnecessarily wordy. This time, you should consider using more direct language, by switching from the verb to the noun: "I intend to improve this paper"

1) Is the word "subject" appropriate here?

Perhaps, and perhaps not. All we know about these "subjects" right now is that we have two examples: "modelling" and "simulation." How are these referred to within your area of expertise? Are they subjects? Areas? Fields? Domains? A project proposal often uses specialized language, and you should use the term that is most fitting for your area of study.

Lastly, there's this:

I want these text to seem more sophisticated...

That's a bad goal, particularly if you're not a native English speaker. You should be striving for simplicity and clarity, not "sophistication." It's a gift to be able to write concisely without muddling up your text with unnecessarily complex words. You don't want to oversimplify your text – if you need to use a sophisticated word, then do so, but you should be doing that to make your message more clear for your intended audience, not just to add an element of sophistication.

Here's my recommendation, based on what I see so far (although I may be misinterpreting what you are trying to convey):

I intend to improve this paper by delving deeper into one of these 3 areas:

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I'm not sure what you have in mind when you say you want to make the paragraph more sophisticated, but if you want to improve it, I would suggest making it simpler. Many people, even native speakers of English who are well into adulthood, believe they should use complicated sentences and long, obscure words if they want to sound intelligent and well-educated. But the goal of language is to communicate ideas, and it's often better to use simple, clear writing that gets your point across quickly and accurately.

For example:

I have the intention of improving this paper

is wordy and indirect, and sounds weak. You can change it to

I intend to improve this paper

which is simpler and more direct, and communicates an active intention ("I intend") rather than a passive state of being ("I have the intention"), which makes it a stronger sentence.

and I want to do this Improve in one of these 3 subjects

There are several problems here. It is ungrammatical: either "Improve" should be "improvement," or you should say "I want to improve...". Also, presumably, you want to improve in all three areas, not just one of them. Most importantly, though, most of these words are entirely unnecessary. Why not just say:

in three subjects

which, again, is much simpler, more direct, stronger, and easier to understand. Putting the two parts together with one final change (from "subjects" to "subject areas"), we get:

I intend to improve this paper in three subject areas

In 10 words we've said the same thing that took us 21 words to say above, and it's a stronger sentence that requires less mental effort on the part of the audience to read. And that's the key to good writing!

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    thanks a lot for your answer it was so helpful. I feel sorry that I should select on answer as accepted answer. I want to choose both answer as accepted answer because they both helped me. – user23047 Feb 21 '14 at 20:00
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    This looks like the best advice to me, and the best "final rephrasing". J.R. seems to have taken OP's erroneous "in one of these 3 subjects" literally, but that frankly makes no sense at all in context. Why on earth would anyone introduce an improvement in just one area by setting out bullet points for two others which are not in fact going to be addressed? – FumbleFingers Feb 22 '14 at 17:35

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