I have a few suggestions on this manuscript, which I have tried to lay out systematically below. The manuscript as it stands lacks support for the position which it is stating. There are also some formatting notes I've included at the end of my comments.
Abstract: You refer to Porfiri et al. (2014) in the abstract and the specimen described in that paper, but do not give a specimen number. Provide a bit more detail about their specimen and include the specimen number in the abstract. You also state that their analysis is based on problematic characters. What are they? You state that there is a character it possesses that is not found in tyrannosauroids. What is it? If someone were just to read your abstract they should be able to get an idea of what you are trying to communicate. "Evidences" is used often by Creationists. Reword that part. "All things considered" sounds awkward.
Introduction: Use a heading to indicate that you don't have a multiparagraph abstract.
Use the specimen number of the Porfiri et al. (2014) specimen the first time you reference it.
Change "large foramens on the premaxilla" to "large premaxillary foramina."
Change "first dentary alveolar compared to more posterior alveolus" to "alveolus" and "alveoli" respectively.
It would be really useful to have an illustration here, especially in light of how you state these are either mistaken or found outside of tyrannosauroidea. A comparison between tyrannosaurioids and other suggested placements showing the location and states of these characters would really emphasize this. Furthermore, Porfiri et al. use more than these three characters to unite Megaraptor with tyrannosauroids.
Did Porfiri et al. assign it to a clade? Or did a phylogenetic analysis they performed find that it fit best in tyrannosauroidea based on those characters? A "just so story" about placement, whether in agreement or disagreement with a placement, doesn't carry as much weight as something testable and repeatable. You need to show how their analysis lacks the support they claim.
You suggest that Megaraptor and its kin are basal coelurosaurs instead of derived allosauroids, as suggested previously, but do not provide any support for this position. This is especially important if you are trying to suggest that coelurosauria is the least inclusive clade for megaraptora. You should be able to access the matricies of the prior analyses and run/modify them yourself in TNT to test these relationships. Otherwise it is a "just so" statement that offers nothing that reading the cited papers already have.
You talk at length about fusion of the nasals for the majority of the second page of the manuscript. Cranial fusion, and osteological fusion in general, is terribly unreliable as an aging tool due to its ontonogenic variability. In this light it can't be used in any taxonomic setting to either support a position or challenge a position. You could talk about the dubious nature of fusion-based taxonomy but it shouldn't be used as part of your argument.
Talking about the distribution of characters across theropods - this, again, would be better demonstrated with comparative illustrations in a figure.
You should look at Zanno and Makovicky (2013) for additional views on megaraptora and its position in theropoda.
Conclusion: You don't have a separate conclusion section. You should. One or two sentences that don't sum up your key points don't really work.
References: Give the section its own heading.
Format: The use of line numbers would greatly enhance the ability of readers like myself to give feedback.
Use a space between the last typed word and the parentheses in the following citation.
There are some sentences that read awkwardly - without line numbers it is more difficult to point them out and offer corrections.
What materials and methods did you use to come to your conclusions? I understand this is a comment or reply to Porfiri et al. (2014) so you may not have "materials" per se but you should have methods. That is unless you have no new data (or new interpretation of the older presented data), in which case this manuscript is based on a "just so story" of your thoughts and not actually scientific. It would be interested to see a paper that looks at the problematic nature of using sutures for taxonomy and ontogeny, with Megaraptor as an exemplar, but you've got a fair bit of work to do to get there in my opinion.