Programming Rock Pikmin to be unique would take a lot of time, actually. Making him a clone takes a lot longer than you think. Not only do they require a new model entirely, they have to be very different from Purple Pikmin to even be considered worth the effort. Otherwise they might as well just make the models and put them on Alph instead of him using Purple Pikmin. I would be okay with this since Alph would look more unique to a degree. At least the male/female costumes for characters have different voices. Winged Pikmin are already used with regular Olimar, and Rock Pikmin being extremely similar to Purple Pikmin already gives little incentive from a developer standpoint to bother with.
Likewise, besides that, he doesn't actually bring something notable that Olimar doesn't already. The focus is on the Pikmin and their overall ability to team up and fight. The Captain is simply like Pokemon Trainer to a degree, where their actual skin used doesn't matter. They could put any Captain as an alt and the overall character would make sense. Really, the only problem with Alph is the skin they used for his ship in his Final Smash at best(It shouldn't still be Olimar's ship). He's already overall playable anyway(which is more than tons of characters have gotten, respectively). Some aren't even alts and are partial references to another character(Daisy, Waluigi, Blood Falcon, one of Pichu's old costumes at best, colors referencing various Kid Icarus characters with Palutena...).
The only difference between the Captain and PT is simply the fact one fights directly. But they otherwise are practically the same idea. They both command a mini-army of Monsters. They both are treated similar to a Class who can be interchanged with any model and still make sense. As long as they have the same overall size(althoug you wouldn't need that for PT since he(or she) is only in the background. They have to only keep the model size and hitboxes the same for a Captain, nothing else).
Maybe next game when there's more time and resources spendable(and more Pikmin show up to help make them higly different from each other). Simply put, it wasn't feasible to expect the Dark Pit treatment for Olimar. Beyond literally the model of the ship used in the Final Smash, there's no tangible difference between Olimar and Alph. They have the same exact abilities. And yes, I am aware Alph's exact proportions in Pikmin are a little different from Olimar, but not enough to matter. Koopalings work fine as an alt for the same reason. They can potentially do the same stuff(Junior may use the Brush, but there's no reason the Koopalings cannot. Just like Alph can certainly ride in Olimar's Ship. That said, again, I think it's silly the sip wasn't reskinned during the Final Smash.). Now, the time part is important; As Alph is actually playable at this time(and it's not simply a costume, but they actually say Alph's name and even label him as that), it'd make more sense to concentrate on characters who aren't more than unnamed colors or bring something fairly new or at if they're going to do clone DLC, takes way less resources than an entirely new model, new attributes, and having to give Olimar 4 new costumes as well as de-programming the ability to go into Alph in this game. It's not feasible from a time standpoint or a character standpoint either. Pikmin is still well-represented by having 5 unique Pikmin to choose from.. If anything, I wish we had more alts for Olimar since the Pikmin themselves are the most important aspect.
I am aware you can make Rock Pikmin unique too. Problem is, that's a lot to do for a character who is still far more playable than palette swaps. One that is recognized fully as his own character. At the moment, it's barely one move that could be slightly different. And a reskinned Final Smash. There's not exactly much to separate Alph at this time. If Olimar's Tether Recovery was still there, then sure, Alph could use the Winged Pikmin. But it isn't. Also, I feel the Whooping Snitchbug idea isn't really all that great as being a unique enough move worth making. That's also a new model, a significantly different one to program for. It's barely different from Winged Pikmin. It doesn't fit as something that would help a Captain either. If they can find the extra time, doing a few model swaps may be nice for Alph's differences from Olimar, but reality ensues that their physical differences otherwise are severely low. Dark Pit at least had a necessary and unique Final Smash. If Alph cannot get one, it's not actually worth the effort. Slight differences alone won't cut it when they're nearly the same move. Especially if again, you requiring multiple new models to make the differences worthwhile.
Apologizes if some points are repeated, but overall, I give a No to him being a clone in Smash 4. Save that for characters who aren't actually playable at all(vets or otherwise). Maybe in Smash 5, that might not be a bad idea, when there's enough to truly separate him without forcing Alph to team up with one of the enemies.