The ironic thing is that Roy vs. Chrom/Lucina is basically a redux of Roy vs. Sigurd/Celice. FE4 was definitely a very popular and well-received game (its the only other FE game in Japan to have reached the 500K milestone aside from FE3), and still among the most popular games in the series in Japan. Sigurd/Chrom are basically masculine blue-haired swordsmen, while Celice/Lucina are feminine blue-haired lords. Sakurai went with the unproven Roy over characters from the very well-received FE4.
While Sakurai said that it was his fire sword that made him stand out more from other possible choices for a second character, I think he felt Roy aesthetically contrasted more with Marth than other lords at the time. I mean I think if we got Sigurd or Celice we would have had most people thinking Sigurd was Marth's dad, or that Celice was Marth's sister.
I think Sakurai still values characters that contrast well with the rest of the roster, and Sakurai saying that no characters have been cut yet (which means Ike could very well be on Sakurai's initial roster), makes me think him and Intelligent Systems had a detailed discussion with the problems of representing Fire Emblem in Smash Bros. Keep in mind too, Sakurai himself is also a big fan of the FE series (he has a copy of FE3 downloaded onto his Virtual Console, and hosted the Iwata Asks for FE11). I am sure Sakurai understands and knows that FE13 was the biggest success the series has had since the GBA days, but also knows of the the massive demand for Roy's return, and the huge backlash from the fans that Ike's removal would bring. I also think Sakurai knows that characters like Roy/Ike (as well as probably Chom/Lucina/FE13's My Unit) won't appear in another game in the series (outside of crossover games and possibly a remake in the case of Roy).
I think Sakurai also understands that the traditional lord arche-type (sword-wielding lord with a cape) has been explored within Smash Bros. quite a bit, and perhaps wants to explore other things the series could bring. I think ideally Sakurai wants FE to have four characters (Marth, Roy, Ike, and a newcomer showcasing something new with the FE series that has not been seen before in Smash Bros.), but whether it will come down to time constraints and possibly hardware restrictions for the 3DS.
Thinking about it, especially in light of the first set of newcomers unveiled for Smash 4. My guess that if Ike returns, Sakurai will most likely be going with either My Unit or Anna for a proper FE newcomer. I think of the three main heroes for FE13, My Unit definitely has more distinction to him/her aesthetically and ability wise than Chrom/Lucina (while also giving those people possibly a female FE character). Its also possible Sakurai and/or IS could have come up with the idea to add in Anna as someone that could not only rep FE13 but the series as a whole. If Sakurai could come up with something like the Wii Fit Trainer as a playable character, its certainly possible that the thought of Anna becoming a playable character has at least been entertained.