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1. The answer here is simple, Dark Emperor and Twinrova were bosses/hazards that had already been revealed. Considering that the Direct was focused on New Information (considering we had gotten details on the Yellow Devil's Mechanics) and that Ridley's shadow was shown in the few seconds that Sakurai was referring to "Other Boss Character Appearances" it is logical that Sakurai would have shown characters that would've been considered "other" or not already revealed at that time such as Ridley, because by the Time of the Direct, Twinrova and the Dark Emperor had already been detailed to an extent, so they were no longer "other" boss characters. Furthermore, in the Direct, Sakurai did not say something along the lines of "Other stages will feature Stage Bosses as well" but rather said "Boss characters will make appearances in other stages as well, not just this one." so his wording is quite ambiguous here, after all, on a technical level, boss characters can appear on any stage in Smash 4 if the player chooses to play as Bowser or Ike (who is technically a boss character for a very short time in FE: Radiant Dawn) and in past iterations the same could be done with Ganondorf. What also needs to be considered is Sakurai's actions in other parts of the Direct, such as his fake-out with the Pseudo Palutena Trophy, while obviously this action was more clear, it still is interesting in the sense that Sakurai did such a thing with a character that was later revealed to be playable.
2. While it may be plausible that Sakurai intends for us to take what he says at face value, numerous counter examples already exist that contradict this desire. For example, a while back Sakurai revealed in a PotD that Phosphora was a trophy, well come E3, it turns out that Phosphora is more than a trophy, in fact she exists as part of the AT lineup. Another example is in his direct teasing of G&W at the end of the Pac-Man trailer where he has G&W on-screen and yet still hasn't confirmed G&W as a returning veteran, what is this if not leading all of the G&W fans on since G&W has yet to be confirmed? If G&W, by some circumstance, ends up being cut, then Sakurai would've completely contradicted himself in saying that he doesn't want to give fans false hope.
3. If our size estimates are correct, then Ridley, playable or not, would be only slightly larger than Bowser. In SSE, Meta Ridley and Ridley, while certainly being smaller compared to some of the other bosses, are still significantly larger than any of the playable characters, Meta-Ridley, being smaller than normal Ridley in SSE, is still at least 2x times as large as DK, and even without his wings, dwarfs DK by a considerable margin, DK being a character that is similar in size to Bowser, who is the largest playable character in Smash to date. Ridley's boss appearances in previous Smash games are still significantly larger than any of the playable characters, so why would Sakurai waste time making him smaller as a Boss Character? There'd be no reason for Sakurai to make Boss Ridley as small as the sizes we've estimated if he is indeed a Stage Boss considering his size in SSBB where he has already appeared as a Boss. After all, Stage Bosses are meant to be intimidating, so if Ridley is a Stage Boss, having more size would certainly help in his intimidation factor. Even in Other M, he is still at least 2x times Samus's size as well. Furthermore, original Ridley when he appears in SSBB, is fought on a stage that is similar in size to the Pyrosphere, so wouldn't he logically be a similar size to such an appearance if he is the boss?
4. This goes back to the fact that Bowser is the largest playable character in Smash Bros. History and that Rosalina also belongs in this category. At their current sizes, both of them come close to clipping through the platforms on Battlefield, and logically Sakurai wouldn't want a playable character to be any larger than these two because it would simply look odd for a playable character to have his head above a platform and his body below. So at maximum, Ridley's size as playable would be similar to Bowser's or Rosalina's. Furthermore, considering Ridley's characteristics, there'd be no reason that he'd be around Mario's size either. Also, it has been mentioned before that the Shadows in Smash 4 are static, and thus stay the same size regardless of a character's position on a stage. Additionally, a Shadow is a representation of the amount of light blocked by a physical object or being, and since shadows are unchanging in Smash, and would logically be very similar to the character's size in the game, little (if any) counter evidence exists at the current time for our estimations to be inaccurate.
5. Certainly, a Stage Boss Ridley appearance could fulfill all of these requirements, but what should be considered is that Smash 4 seems to be breaking a lot of the trends of the older games. For example, in past games, Bowser was always the incredibly slow, incredibly heavy, and hard-hitting character, but in Smash 4, he is significantly faster, has had a notable posture change and is altogether completely different from how he used to be. Furthermore, Smash 4 has also eliminated transformation characters, a characteristic that was in Melee and Brawl. Also, the game speed, the higher prominence of ground-based tactics, the killing strength of throws, the FD stage forms, etc. are all things that notably differentiate this game from any of the earlier Smash games. So who's to say that they'll not break such a trend with the Metroid Stage Characteristics?
6. While Sal Romano's source has certainly mentioned almost all of the characters that have been revealed as Newcomers, it has to be kept in mind that he has not revealed ALL of the characters. Such an example would be Rosalina, who wasn't included in either of the leaks and still was revealed as a newcomer. Furthermore, interesting parts exist within the leaks to suggest that Sal Romano's leaker may not know all of the characters to be revealed as newcomers. For example, in his 2nd leak, he mentioned a "Pokemon from X and Y" but we know now that the roster was already decided on in early development, so at this time there would've been nothing preventing him from writing Greninja aside from the fact that he only knew that a "Pokemon from X and Y" was to be included, and not which specific one. This along with the Rosalina counter example further support the idea that Sal's source may indeed not have access to all of the planned newcomers for Smash 4. So to be blunt, it is compulsively ignorant to automatically assume that Sal Romano's source has leaked all of the remaining newcomers to be included in Smash 4.
7. Again, Smash 4 has shown that Sakurai and his team are willing to break from the formula that has been present in past Smash games, so it plausible that Sakurai's view on the Metroid franchise has changed this time around. This also goes back to the idea that the character roster and other certain characteristics such as bosses for Adventure Mode are decided early in development. In Brawl, since SSE was supposed to be this epic battle between the heroes of the Nintendo Franchises and the villains, who were working under Tabuu, it is logical that Ridley was simply decided as one of the non-playable antagonist characters. It should also be considered that during that time, Sakurai thought that the implementation of Ridley as a playable character would've been impossible, but as Smash 4 has shown, Sakurai is prone to going back on his past statements (such as his statements about an Animal Crossing Representative "not fitting" because they weren't from a universe with tons of action and fighting) so it is plausible that this time around Sakurai wants to move past the idea of "two playable Samuses and their arch-nemesis as boss character."
The above statements are my responses to each of your questions.