I decided go into some details that I think are important in regards to speculation pertaining Fire Emblem in Smash Bros.
On Sakurai and Fire Emblem:
Sakurai has called himself a big fan of the Fire Emblem series. He has gone as far as to be the interviewer for the Iwata Asks feature for Fire Emblem Shadow Dragon. Sakurai has stated that his favorite character in the series is Nabarl.
On Marth in Smash Bros.:
Marth is the face of Fire Emblem in Japan. Fire Emblem Monsho no Nazo is to Fire Emblem as Ocarina of Time is to Zelda or Star Fox 64 is to Star Fox. FE3 is by far the most popular game in the series in Japan, and sold by far the most copies. Marth was also the main lord for four games in the series (two games prior to Melee). Marth was also by far the most requested character to represent the Fire Emblem series in a poll that Sakurai had prior to beginning development on Melee (by comparison, Celice got only four votes, while Sigurd and Leaf only got two votes each).
On Roy in Smash Bros.:
Contrary to popular belief, Roy was not placed in at the request of Intelligent Systems, but rather it was Sakurai's idea. Sakurai said that placing in Roy was his idea and that he did it primarily to promote "not just a new game, but the series as a whole."
On Ike in Smash Bros:
Sakurai stated in an interview with Famitsu that Ike got in Smash Bros. because he wanted Fire Emblem to have a new character from a more recent installment and he did not know who to put in. Sakurai went to Intelligent Systems for help regarding this matter, and Intelligent Systems suggest Ike to Sakurai. It is important to keep in mind that FE9 was the worst selling game in the series in Japan (yes, even selling more poorly than Thracia 776). The only three games in the series to sell below 200K in Japan were FE9, FE5, and FE10. Another interesting thing to note is that Sakurai said he originally planned for Ike to have the Ragnell's ranged attack, however, he felt this made Ike unbalance so it was scrapped.
On Roy being cut from Brawl:
Mewtwo and Roy being cut was likely the result of time constraints. Sakurai has gone on the record to say that he intended more characters to be in Brawl's roster but was not able to implement them due to time constraints.