First, let me make something clear for those who do not read the full article: Chrom being on the project plan was never something that was said by Sakurai directly. However, after looking through Sakurai’s latest books, the other translators and I at Source Gaming have concluded that Chrom was very likely to have been included in the original project plan. Before going into the implications, I would like to take a moment to review all relevant quotes, provide the sources and the original Japanese (on the bottom of the post).
A. The first piece of evidence for this claim comes from Sakurai’s quote under Robin’s slide. (Translation by Masked Man) Here he states
↑ After everything is decided, the staff works as a single unit to create everything as planned, but unfortunately some characters still end up slipping through the cracks. 
The placement of the quote is suspicious, but by itself it does not confirm Chrom was in the original plan. Please note of the date for these slides were April 26th, 2012.
These slides are incomplete. “Smash Tour” is not included in the Wii U Features section, and a lot of the “New Fighters” are missing: it’s obvious that some slides were not included. Therefore, the lack of a Chrom slide is not proof that he was or wasn’t on the project plan. The slides as a whole are irrelevant in terms of proof as the proof exists elsewhere.
Here is where additional comments made by Sakurai in the “Looking Back” sections of his various Famitsu Columns come into play.
B. Here is the reflection of the CEDEC 2012 reflection (Translated by Soma), Vol 409:
Interviewer: Didn’t you deliver this keynote during a really busy time?
Sakurai: When was it again?
Interviewer: Um…around August 20th, 2012.
Sakurai: Oh, that was a really busy time! (laughs). In terms of “Smash for 3DS/ Wii U” development, that was right when I was explaining character specifics and movesets to the staff. And Robin had just been decided…
Note: The rest of the interview is about the CEDEC 2012 talk. Stay tuned for a full translation!
C.”Are the Characters Dancing?” vol 430 (Full translation will be posted when it’s ready)
Sakurai: Here I give the example of Chrom. When it came time to decide on a character from “Fire Emblem: Awakening”, I had even thought of a moveset for him. However in the long run, he was just in between Marth and Ike, so he wasn’t added. However, when I thought of the “Sword and Magic” concept for Robin, it was an character oozing with personality.
Interviewer: In the end you settled on Robin and Lucina. Did you come up with this characters immediately?
Sakurai: Let me see. How long “Immediately” is can be a range depending on your way of thinking. Wii Fit Trainer was especially easy [to come up with]. 
Note: In the rest of the interview, Sakurai talks about Wii Fit Trainer’s inclusion.
D. Here is a translation of Lucina’s and Robin’s Famitsu column (Vol 457).
The most relevant quote is the following (translated by Masked Men):
I suspect a lot of you will ask: “What? Not Chrom!?” Of course, Chrom is quite popular, being the protagonist of FE:A and all. However, I chose Robin and Lucina, and I will elaborate on my reasoning.
Later on, Sakurai continues:
I played all the way through FE:A and really wanted to include a character from that rich cast in Smash Bros. Naturally, I considered adding Chrom to the roster, but the decision wasn’t easy by any means. At the end of the day, Chrom would just end up being another plain-old sword-wielder like Marth and Ike. Compared with other characters, he lacks any unique characteristics.Conversely, when the idea of including Robin came to mind, conceiving the character was so easy that I immediately saw how it would work. 
E. Lastly, there is Palutena’s Guidance for when Robin is on the field:
(Japanese version on the bottom of the post)
…which is essentially a rehash of Sakurai’s reasoning for not including Chrom.
The important line to take away from these Guidances are:
Chrom: “Certainly more useful than a simple swordsman like myself”
Viridi: “Plus, you and Ike are too similar. No point in having two characters that are pretty much carbon copies. Am I right?” (See the translation column below, for the original meaning)
Palutena: “What’s more, you don’t have an Aether recovery move like Ike does, do you?”
Please note, that the Japanese version is slightly different, and in some ways is less harsh to Chrom. I have put the differences between the Guidances in the end of the article.
There is a major issue with Sakurai’s timeline. That is, if Robin was decided in August 2012(B), then why was he in the project proposal plan (A) for April 2012?
A possible explanation is that Chrom and Robin were both in the original project plan, as evident by Robin’s inclusion in the April 2012 slideshow (A) and Sakurai’s comments about coming up with a moveset for Chrom. However, after coming up with a moveset, which took until August 2012 to essentially complete, (B), Sakurai realized that Chrom did not have any defining characteristics (D). It was because of this issue that Chrom was dropped from the roster in August, 2012 (C), only to be moved to Robin’s Final Smash. Once Chrom was dropped, Sakurai fully committed to Robin.(B). Sakurai reflects on these events in his Famitsu column on Robin and Lucina (D) and the Guidance (E). It is also possible that he had a slot for a Fire Emblem: Awakening character reserved, and that the choice was between Robin or Chrom.
We know that Chrom could not be an alt for Ike (E) or Marth because he had very different moves/ lacked the ability to directly copy their moves. Lucina’s inclusion in the roster was solely because of different properties that she had vis-a-vi Marth, and the development team having some extra time.
In my opinion, this essentially confirms Gematsu. Take note that since a Rhythm Heaven emblem reference (full details here) was found alongside other character emblems that all of the characters from Gematsu have either appeared in Smash or are confirmed to have been planned in some slight way. In the very near future we at Source Gaming will be taking a closer look at the Gematsu Leaks and discuss the full history of the leaks with possible explanations for why some characters were not included and what this means for future Smash games. We have reached out for Mr. Sal Romano for a comment, but as of right now, he has not replied to any of our requests.
Differences in Guidances:
(Note: bits that aren’t mentioned have little to no differences between them)
|Character:||Japanese:||Loose Translation:||English Localization:|
|Pit:||パルテナさま、意外な人が参戦してますね。||Lady Palutena, an unexpected* person joining the battle!
*意外 can mean unexpected, strange
|There’s something weird about this fighter, Lady Palutena.|
|Chrom:||おいおい。勝手に怠け者にしないでくれないか||Wait a minute! Don’t go around calling me lazy.||I’m no idle layabout.|
|Viridi:||クロムが出てもアイクとキャラがかぶりそうじゃしのう||If you showed up, you would probably just overlap with Ike.||Plus, you and Ike are too similar. No point in having two characters that are pretty much carbon copies. Am I right?|
|Chrom:||この剣にかけて、ルフレは俺が守る||With this sword, I will protect Robin!||And then you’ll taste the bitterness of defeat!|
|Viridi:||カッコいいことと言っておるが 出場はスマッシュボールが必要なのじゃろう？||You are saying some cool lines, but,don’t you require the Smash Ball in order to participate [in battle”]?||We know you’re trying to play the hero and all, but you can only join in if Robin gets the Smash Ball, right?|
|Chrom:||…….だからルフレ、ボールを拾ってくれ。頼む||……Please get the Smash Ball, Robin. I beg of you.||You’ll taste the bitterness of defeat! ..Right after Robin gets the Smash Ball.|
The English localization team probably wanted to make the dialogue more ‘funny’ as it makes Chrom more of the butt of the joke.The original Japanese is:
あとは可能な限り、スタッフが一丸となって作り込むが、残念ながら漏れるものもいる。 The original Japanese is:
桜井:そりゃ、ほんとにタイヘンなときだ！（笑）だって、「スマブラfor」で言えば、キャラクターの仕様やワザをスタッフに説明している最中ですよ。ルフレは参戦が決まっていたし….。 The original Japanese is:
桜井 ここで例として”クロム”を挙げます。「ファイアーエムブレム 覚醒」から何か出すと決めたとき、クロムのワザも考えましたが、どうしてもアイクとマルスの仲間のようになってしまし、まとまりませんでした。しかし、”剣と魔法”というコンセプトでルフレを考えたら、非常によい個性がにじみましたね。
桜井 そうですね。 ”すぐ”がどれくらいは、考えかたによってピンキリですが。とくに、Wii Fit トレーナーは楽でしたね。The original Japanese is:
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Mains: Yoshi (64), Game and Watch (Melee), Wario (Brawl), Wario/Pac-Man (Smash for 3DS/Wii U)