Before I explain, I should explain why I think Flowey will appear.
HE REUSED TORIEL
HE REUSED UNDYNE
HE REUSED ALPHYS
HE REUSED ASGORE
HE REUSED SANS
HE REUSED GERSON
WHY. NOT. FLOWEY.
Even the ones that haven’t appeared yet have been implied to exist.
Of course there’s the problem of Flowey being Asriel, but in the original Undertale, they’re treated like separate characters. Asriel in undertale even says not to look at him as Asriel when he’s Flowey.
Now, there’s the problem of how. I personally think there’s a simple-ish answer.
You know the yellow Flower in Asgore’s garage? The one in the center of the rest? I think that Flower specifically will have been nicknamed “Flowey” by Asgore.
Of course, Flowey needs a motive. Here’s a few ideas I have for that:
Flowey is bored of being confined to the back of the garage, and seeks ways to escape.
Flowey is fed up with Asgore’s current state, and his taking matters into his own vines.
Flowey wants the SOUL so that he gain our power.
Flowey doesn’t want Kris to leave because for reasons slightly reminiscent to his relationship with Chara in Undertale.
As for his role in the game, I think he’ll be a penultimate chapter boss. Considering Flowey is smack dab in the center of of the garage, I don’t see him being a secret. It would be pretty difficult to pose him as a supporting character without drastic personality changes considering how he was set up in Undertale. However, he shouldn’t have the power to reset and such, so maybe?
Anyways this is just a theory I’m in confident in. Rebuttal is welcome.
I dont doubt that they will lay on the Flowey allusions pretty heavy, but I do doubt we'll get actual Flowey. I strongly assume those flowers will become important darkners in the very likely Flower King dark world, and it wouldn't surprise me for the golden flower to be their "leader" of sorts. Maybe even with a boss fight involving sequentially recruiting the other flowers, alluding to taking back the souls from Flowey.
But Flowey's whole character and personality originates from Chara and Asriel's failed plan to gather human souls, and I don't think it could just be transplanted (heh) into Deltarune without that backstory.
Flowey will almost certainly have a role if a dark fountain allows you to access Asgore’s shop in the dark world-Flowey would likely appear as a Darkner.
Also, since the idea of Flowey as a separate character from Asriel came up, Flowey and Asriel are fundamentally the same person, but, by having no emotional attachment to the people in the world and seeing it all as a script repeating, he went from an innocent and kind person to a monster
I think this is what makes him such a good metaphor for the player
When Asriel says not to think of Flowey as him, I think he just means not to associate the memory of Asriel with anything Flowey did wrong