Yep. @
thethirdkoopa had sources with inside sources apparently, and he leaked me all kinds of stuff back then. We were among a handful of the few people who knew pre-Brawl what the 41st stage was (75M) that weren't involved in development.
Apparently Roy and Mewtwo were both cut early in development due to everything stacking up, namely the SSE (which I'll dive into later). Mewtwo was obviously cut a few months later than Roy, but both were kind of an afterthought. Actually, the characters were an afterthought. Well over 60% of development time, money, resources, and efforts were focused on the Subspace Emissary. At some points in development that's all anybody worked on.
Eventually though, the development team reached a point where the SSE was too big and too expensive to continue. It made them go over budget, but if they really wanted to do what Sakurai envisioned it would have been a huge money drop into something that quite frankly was not fun to play for more than a handful of players.
With that said, Roy and Mewtwo were likely very much liked as characters to be kept that long. It isn't even a bit surprised they're back as Smash 4 DLC.
I'm a bit fuzzy on the dates and times of stuff, but I think all of the Forbidden 7+any other characters that aren't Roy, Mewtwo, or playable in Brawl were cut within a few months of development, and Mewtwo and Roy were cut within a year. Sakurai's whole "the roster was completed except for Sonic in 2005" thing was either inaccurate or obviously a lie to hold back a few exceptions (I don't blame Sakurai for not wanting to reveal that). As we know, in addition to the Forbidden 7 the idea of Pac-Man, Miis, Villager, Takamaru, and Nintendogs as playable characters were thrown around (although we don't know if they were produced or pre-produced ideas at all, only considered).
Also, a detail worth sharing, but Mewtwo was seen as "more trouble than he was worth." He was apparently very glitchy when ported over from Melee, in part because his Melee build... was filled with technical issues. So, that's a major reason Mewtwo was cut. Had it not been for such difficulties and poor design build, they could have just reused a lot of Melee assets for Mewtwo (or easily recreated them) much like other Melee veterans in Brawl. That's a big reason why in Smash 4 Mewtwo, although using all the same moves as Melee, has completely different hitboxes and functionalities on them; because everything is different.
That's not to say Roy didn't have issues, but honestly, he was never the priority Mewtwo was. He was always seen as a "added bonus" kind of character, whether it be Melee, Brawl, or Smash 4, which is why he was held off for DLC in the latter game.
I've heard this hypothesis before, but I've never heard it backed from people with inside sources. I do, however know that like 40% of the SSE was cut. We obviously know the Halberd getting stolen from Meta Knight by Dedede (who was betrayed by that evil alliance) was cut, as was I think some early Ness, Ike, etc parts. There's also many characters that just sort of happen to "be there" without any sense or reason, like Luigi, Yoshi, Ness, Ike, Ganondorf, Sonic (that was obviously put on at the end), and kinda sorta Olimar.
I have heard from people with more sources than I had that Jigglypuff was never planned to be cut, and that any such statements about her being on the cutting block are false. I think I heard Jigglypuff is where she is in the character listing (towards the end) because she was finished near the end of development. Considering all of her properties from Melee are changed (whereas some characters keep a lot of properties), this isn't surprising. She's also a very simple character to make, so holding her off for the end when you have just a few months is much more doable than say Marth.
Personal hypothesis on the situation: Wolf may or may not have been considered to be cut or even cut, but there's no data outside of the character order listing (which due to my Jigglypuff reference, makes such an argument invalid) that Toon Link was cut. There's also a chance that the completion of these 3 characters was pushed wayyyyy back for Sonic (who wasn't added until 2007; like a year within Brawl's launch). Heck, they may have been a big part of the 2 (or was it 3?) delays of Brawl was due to them not being ready.
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Oh, and for the record, dozens of characters are considered that never make it. Literally dozens upon dozens. Of course, "considered" doesn't mean produced ala the Forbidden 7, the Ice Climbers in Smash 4, etc. Note that there's different levels of production, and different steps of game design, and that each of these categories can be very different from one another.