I was quite a fan back then, and you remember it slightly differently than I do. Yes, the new types were important, but Most important? No. The absolute most important thing was that they were adding pokemon,
I think 'that they were adding more Pokemon' was to be expected, almost like a sequel to a racing game coming out and saying 'it's going to have new courses!'. That's how I remember it, I don't recall any of us, myself included, being blown away or shocked
that they were adding more Pokemon, we were interested in what
kinds of Pokemon were being added.
The difference with Fairy type is that it happened after three generations where no types were added. That makes it a huge deal.
Mega evolutions, yes, equally so.
I think the Pokemon fan community felt a little underwhelmed by the announcement of the new fairy type though. The games are still primarily targeted towards boys, and "Dark" and "Steel" were exciting to hear for us, but "Fairy" type didn't seem to gain a lot traction. Everyone was busy obsessing and swooning over Mega-Charizard. Some 12 years later though, the fan base now consisting of people who only just started playing pokemon within the last generation or two, so the addition of the new type might not carry as much significance to those who haven't been with this series since it debuted, who are fewer and fewer in number as the years go on to be sure.
Also, just some debating notes: You mention gen six getting many new things, but your big points were the new system and the fully 3D models. Well, every gen but five was on a new console, and these may be in 3D, but that gen was in COLOR.
In addition, you state breeding, shinies, and held items as symbols of gen two (Id add in the time mechanic)... you rather admit gen two added a ton.
Sorry, let me clarify a little. Gen2 may arguably have actually added more staple and iconic things to the series then any other generation (assuming we aren't counting the first of course), but virtually all of it are things that had a more pokemon-meta significance, mechanics, etc. Let's separate the changes into things that did or did not have a relevance to roster additions in Smash. First, the things that didn't:
Day/Night cycle. Awesome concept at the time, could have been considered perhaps to be incorporated directly in the form of a Pokemon stage that alternated between day and night. You could argue that it could indirectly be represented as a playable fighter that (in the pokemon games) evolves based on the time of day. Even still, I don't think that particular sub-characteristic of the new day cycle was as hyped and emblematic of the generation as the new types were.
Breeding. As above, very important addition to series, but frankly, I don't think this was realized until sometime during the life-span of gen3. Back when Gold/Silver were released, I don't remember anyone particularly caring about breeding, there was no competitive scene or developed meta-game at the time, no one knew about EVs and IVs. We were all like, 10 - 12 years old still. Most people didn't have the internet (at least where I lived), so everything we discovered about the games were through rumors and that one kid on the block that got the magazine. So there just wasn't a robust scene of people playing competitively who could get all of the base stats at the click of a button on serebii and micromanage and plan out the perfect team of flawlessly EV-trained pokemon hatched from the egg. That was all a pointless effort back then, why do that when you can just go catch one in the wild? Breeding wasn't an attractive feature at the time. So again, this feature was huge, yes, but only in retrospect I'd argue.
Held items. Staple addition, albeit a little minimal at the time. Still, no real direct way of representing it in the Smash roster. Wasn't hype-train fuel either.
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Ok, here are the features that would have been relevant to Smash, essentially, changes made to the Pokemon themselves. There was fundamentally four things:
Happiness. I don't think a lot of us knew about this pre-release either, but it did catch on fairly quickly as we learned it was what we had to do to get that bada** looking new Golbat evolution. Again, could only really indirectly be represented in the Smash roster by 'a pokemon that evolves through happiness', which they technically did do, but more on that later.
Genders. They could have featured this in Melee's roster if they wanted to as a pokemon that was exclusively one gender (which wasn't
technically new remember) All in all, not something influencing Sakurai's decisions for Melee obviously.
Shinies. I'm not certain anyone knew about them until the game came out and we got to the Lake of Rage for the first time. Actually, shinies as we understand them today were really not a big thing back then because most of us didn't know
any pokemon could be shiny, we figured the red Gyrados was a pallette swap that just applied to that one encounter, or if one of us did by some miracle stumble across one, and even notice that it was shiny:
That was us. But anyway, could be represented in the roster as color swaps, which may very well have happened, but as it applied to all pokemon, not something to influence Sakurai to choose any one particular pokemon for that reason.
And finally, the new types. This one should have been the one that got Sakurai's attention. It was the most visible, known and excitable thing to be added or change about the pokemon themselves. And there were a few good, Smash-friendly choices too. Scizor, added even more to already popular Gen1 Scyther. Sneasel. And (how awesome would it have been?) Tyranitar. The rest: too birdy, bally, or quadrupedally. But workable options for sure. Alas, Sakurai went with Mewtwo, who was a still very relevant Gen1 'mon and was intended to be in SSB64 anyway, so that was fair, and then of course...
There are many theories floating around about why this choice was made. A lot of people believe the Pokemon Company was (and still is) strong-arming Sakurai into featuring the pokemon they wanted to promote for the Anime, Merchandise, etc. I believe it was possibly some of that, but more over, Pichu was a convenient clone to flesh out the roster under the time and resource constraints. That said:
as representation, he completely signifies much of this: he takes on your own standard, and represents the idea of breeding, as well as the phenomenon of baby pokemon, and a new kind of evolution: happiness.
This, I don't believe is why he chose Pichu. Pokemon representation in Smash has always really been about that one or two pokemon that are recent and/or very,
very popular. I don't think Sakurai is looking at the same details of the Pokemon series (in this particular case) as the fans of that series are, but rather, the big, broad details. One popular pokemon from the newest games, and one or two majorly iconic classics (Charizard, Mewtwo, etc). That's probably what he is primarily concerned with. Other new things are just filler or details at best, be it baby pokemon, breeding, or indeed even mega-evolutions. I think they are in Smash4 for rather incidental reasons. It's just plain obvious given popular pokemon that are bound to be in smash, were similarly bound to be given mega-evolutions, and it was just an obvious thing to do as a final smash, they were so perfectly analogous. But I don't believe Sakurai in any way, went
out of his way to put those into the new smash.
So that leaves us with poor old Jigglypuff. As has been said, she arguably has just two things going for her. New type, which my thesis paper above discusses, and O12 status, which honestly, has mainly been contrived by the fans. The development of Melee was so short, hectic and expansive that there wasn't time to cut any of the original characters, only to fill up as much as they could muster to make it big and impressive. Next, there is only Brawl. And maybe the O12 all surviving the second transition means something, or maybe Sakurai didn't feel any of them needed to be cut
at that particular time. But of the O12, Jigglypuff is the least iconic as a character, least important to her franchise and has the most competition within her franchise by a long shot, and finally, is the singly least popular character in Smash entirely as of Brawl (if I remember correctly). It's just a matter of whether Sakurai places the same sentiment on the original cast as some fans so, or if he is really thinking about the status of the characters as "all-stars".