The Rambam notes that Moshe Rabbainu and his court ordained the Mitzvah of publicly reading of the torah during public prayers.(Hilchot Tefila,Chapter 12.Law 1)
In order to observe this mitzvah there are a number of essential concerns.
1.  The Sefer torah must be kosher. Namely , It must be written correctly on parchment and no letters added  or missing.Violation of this rule invalidates the Mitzvah.
2. A  Sefer Torah does not have any punctuation or notes for vowels or proper pronunciation.  Should it be read in a way that the reading error changes the meaning of the  word, the mitzvah is not observed. (This rule obligates the reader to spend time studying  to be able to read  the Torah without mistakes.)
3.Tradition has it that there are notes to mark the proper chanting of the Torah. These notes are called “trope”. Of interest is that should one simply read the words of the Sefer torah portion without chanting any of the “trope”,the Mitzvah would still be observed. It may appear and be heard as a violation of tradition. It may be derided for being a bizarre deviation. Yet,the Mitzvah is observed even without the accepted chanting of the Torah. (See Aruch HaShulchan, Orech Chayyim 142:  who explicitly so rules. It is, therefore, preferable and an enhanced means of observing the mitzvah by learning by heart to chant the portion with the proper ‘Trope”. Should, however, one not chant with the “trope” (bid’ieved) the Mitzvah is still observed. Many times I have personally been at synagogues wherein the regular Baal Korai was absent . In addition, no one was available who was able to read the Torah with the proper “Trope”. In such circumstances volunteers would read the portion without any reference to the “trope”.The custom, moreover, in many Hassidic (Shteeble’s) is for the Baal Maftir to say the Haftorah silently or all together with the congregation. As a result many who frequent these places do not  even know the proper  “trope”. In fact when they attend major large synagogues they refuse to accept Maftir for they contend that since all are attentive to the person reciting  the Haftorah they are ashamed to recite it without “trope”.
4.For a Bar mitzvah youngster to read without  “trope” would generate the following concerns. Why is he deviating from tradition? Was he simply not able to memorize the “trope”? Since he cannot chant, perhaps the synagogue should not have permitted him to read the Torah. Was there not sufficient time to learn how to chant correctly? Why should the congregation have to miss out on hearing a proper chanting of the Torah? Though these are decisions that individual synagogues may determine for themselves, according to Jewish Law, the reading of the Torah without chanting does not invalidate the Mitzvah. Some children simply do not have the ability to memorize both the reading as well as the chanting. Compassion is also a time honored Jewish custom.
 

As for what a certain bar or bat mitzvah student should do in a particular congregation, I would encourage you to reach out directly to that congregational rabbi.

 

The chanting of the Torah is an ancient practice. There are lots of precedents and reasons offered, as you will see below. That said, there is also evidence that some communities may have opted to read instead of chant. In particular, the Reform Movement has a history of reading the Torah for public services. Here is a brief review of the data, pro and con.

Ezra introduced the practice of reading the Torah aloud, as we learn in the book of Nehemia. It is not known if the Torah was chanted in that period, although the chanting of sacred texts was a common practice in the ancient world. There are accounts that in ancient Alexandria the Torah was read with simultaneous translation, which suggests that it may have been read rather than chanted in that setting.

Based on a few passages in the Talmud it seems that chanting was the norm. B.Nedarim 37b records a debate regarding pay for one who teaches Torah to a child. Since you may not be paid for Torah study, the text suggests that the pay was for some associated task, such as teaching the cantillation. This provides evidence that the practice extends back to that time, and that it was a common component to the teaching of Torah for children. Rabbi Yochanan, a third century Palestinian Amora, asserts that chanting is so important that one who opted not to chant offended God. He taught that anyone who studied Torah or Mishnah without chanting the text conformed to the dark words of Ezekiel: "Moreover, I (God) gave them laws that were not good and rules by which they could not live" (Ezekiel 20:25; BT Megillah 32a).

Jacob Neusner, in Judaism's Theological Voice:The Melody of the Talmud, argues that from the very first moment at Mt. Sinai we hear God's voice as singing because that puts us dramatically in the present. Words can be read over and over, but music “comes into being at the moment of performance”, hence when we hear the Divine word chanted we recreate the experience of Mt. Sinai. He writes, “singing serves to transform secular study into sacred service.” Chanting, he asserts, transforms the experience of hearing Torah in a way that reading does not.

On the other side of the coin, a Responsa from the Central Conference of Reform Rabbis includes a history of reading the Torah at public services. (http://data.ccarnet.org/cgi-bin/respdisp.pl?file=153&year=carr) They note that “Israel Jacobson, the founder of the Reform Movement, sought to remove the cantillation along with other forms of music which had become distasteful, as for example, the singing of the cantor accompanied by a bass and a soprano, one standing on each side and harmonizing.” Rabbi Mark Washofsky notes in his book, Jewish Living (pg 28) that “Rabbi Isaac Meyer Wise expressly provides that 'the sections from the Pentateuch are read in a style agreeable to modern delivery...” I understand that to mean that reading or chanting is acceptable. There are many Reform congregations which prefer the reading of the Torah today.

Here are two reasons I have heard for why a community may prefer to read Torah. First, there may not be a qualified teacher who can help readers with the nuances of this art. It is not simply a matter of reading notes off a page, not an easy skill in its own right, but of being able to make the notes and the words fit appropriately. Second, there are many places where a simultaneous translation is offered alongside the reading and the two fit together better when the Torah is read. This practice helps the listener better understand the text that is being presented, adding an element of Torah study alongside that of Torah reading. For many places this is a desirable goal.

This brief history suggests that precedents exist for either reading or chanting the Torah during a public service. It does not, however, say that the decision resides with the individual. Different communities have different standards and when an individual or a family join that community they implicitly agree to abide by those standards. It would be disruptive if one who regularly attended services heard reading one week and chanting the next. Continuity adds to the spiritual impact of a service.

There are occasions when a student simply is incapable of learning certain prayers or chants. In those cases (rare in my experience) I would hope that a community would find a tactful way of accommodating the needs of that individual. Bar or Bat Mitzvah should not be an occasion for trauma or exclusion. Still, the decision should come from a dialogue that considers the needs of the student and the custom of the community.