Sets a very bad precedent. Giving him a pass because he's "nice" opens the door to giving a pass to many, many others who may not be so "nice". Like electing a really good guy who isn't 35 yet. Only that is not as bad, because eventually he'll become 35.
It's more than just that. Reading stuff written in the founding era leads me to believe they may have handled it in the same way. Look at these comments from General George Washington for example.
“You are not to enlist any person who is not an American born, unless such person has a wife and family, and is a settled resident of this country.” George Washington, Given at headquarters, at Cambridge, this 10 July, 1775.
“You will therefore send me none but natives, and men of some property, if you have them. I must insist that in making this choice you give no intimation of my preference for natives, as I do not want to create any individual distinction between them and foreigners.”
“The General has great Reason; and is highly displeased, with the Negligence and Inattention of those Officers, who have placed as Centries at the out-posts, Men with whose Character they are not acquainted. He therefore orders, that for the future, no Man shall be appointed to those important Stations, who is not a Native of this Country, or has a Wife, or Family in it, to whom he is known to be attached. This Order is to be consider’d as a standing one and the Officers are to pay obedience to it at their peril.” - 11 Fox, Adj. Gen. of the day. 9
Not conclusive, but indicative. Other quotes showing Washington's disdain for foreigners here.
Another example would be this excerpt from the 1783 version of the Virginia Citizenship act.
and that all persons, other than alien enemies, who shall migrate into this State, and shall before some Court of Record give satisfactory proof by oath (or being Quakers of Menonists by affirmation) that they intend to reside therein, and also take the legal oath, or affirmation, for giving assurance of fidelity to the Commonwealth (which oaths or affirmations the Clerk of the Court shall enter on record, and give a certificate thereof to the person taking the fame, for which he shall receive the fee of one dollar) shall be entitled to all the rights, privileges, and advantages of citizens, except that they shall not be capable of election or appointment to any office, legislative, executive, or judiciary, until an actual residence in the State of two years from the time of taking such oaths or affirmations as aforesaid, nor until the shall have evinced a permanent attachment to the State, by having intermarried with a citizen of this Commonwealth, or a citizen of any other of the United States, or purchased lands to the value of one hundred pounds therein.
My understanding is that Rubio's Father (already a long time resident) had initiated the paperwork prior to Mark's Birth to become a citizen. His mother had already become a citizen prior to his birth. Given that the mother had already become a citizen, and the father had filed to become one, it is evident that the Father intended, and indeed did became a citizen. It is apparent to me that the family met the spirit of the law if not the letter. That his father didn't complete the process before his birth is in my mind a technicality.