The reason Olimar is top tier in the current metagame is that the current ruleset is all of Olimar's counterpick stages as the only stages. ICs are the same way; they're "top tier" in the game of few stages but not really top tier in the full game (and weren't considered top tier back when more stages were commonly legal). Both are good characters either way, but they're not like MK who is top however you slice it. Also, honestly, MK is the only poorly balanced good character in Brawl; I wouldn't hesitate to call someone like Diddy a well designed, well balanced character either. The low tiers needed buffs moreso than the high tiers needed nerfs.
Also, no, there's no reason to assume he's down to three. I know some of you guys don't really know the technical side of this very well, but Olimar's pikmin are not analagous to Nana in any real way. They're more analagous to the projectiles Link can spawn than characters (and programmed the same way as Link's projectiles in Brawl); they're incredibly simple, and you could probably handle several dozen of them before it was as burdensome as a single character (wih the added benefit that Olimar has a relatively simple character model and no additional articles). The 3DS is also not nearly as weak as some people believe; it's actually a more powerful system than the Wii. Either way, when he said multi-character characters, among veterans the only ones that qualify are Pokemon Trainer (though the background character is VERY simple and wouldn't pose a huge problem, still far more complex than a pikmin) and Ice Climbers so I suspect that his use of the plural may refer to some newcomer concept that's giving them a lot of trouble. I understand how from real world logic Olimar might seem to be included, but from a technical standpoint he's just not especially since we've already seen that the 3DS uses scaled down models versus the Wii U so if Olimar were really giving them problems they could just remove detail from the pikmin until they were very easy to render (the HD pikmin in the Wii U version are quite nice looking, but we know they won't look like that on 3DS).
From a gameplay standpoint as well, three makes no sense because Olimar has a confirmed to return move that uses two. If Olimar has a full stock of pikmin and does two down smashes in a row, will he only get one side of the attack on the second one in your hypothetical version of the game? That would be super awkward and would make playing the character just plain weird in a bad way; I don't think Sakurai would have left any multi-pikmin use moves in the game if he were really reducing it to three because it's just too bad for gameplay. I suppose there's no direct evidence that he didn't make this bizarre design decision, but there's not a single reason whatsoever to believe he did and several logical reasons to believe he didn't so the speculation to this effect is just silly. I didn't mean to go in so hard on this point, but seriously, if you believe this to be true you're very misinformed.