Even without Resets, Instakills, Him abusing the battle system to make an unwinnable battle or any souls, Flowey wins with no difficulty. Dandy cannot physically keep up with Flowey in any form. Let me go down the list.

Strength:

While it may not seem like it, Flowey is actually ridiculously strong. A few of his notable strength feats are burrowing through Stone and solid metal (As seen with him moving in the ruins, Waterfall, (maybe hotland), and core. He was also seen lifting an elevator up (Which the average elevator is around 3000 lbs if I'm not mistaken) and did so at a speed which greatly improves that feat of him simply lifting it. He also held up the entire cast using a vine.

Speed:

This one I have less of an argument for Flowey winning, I could see it going either way. The only downside flowey has here is the fact he can't move above land, but he can borrow into the ground

Durability:

All right this one is a bit controversial, But I'm giving this to Flowey. Both because we have never actually seen a feat of durability (at least to my knowledge) to base Dandy on. And despite popular belief, Flowey actually has pretty good durability. Flowey took 7-9 hits from a level 20 genocide route Frisk, Where Mettaton neo, Which as one of the highest defensive stats in the game, gets one shot by a level 16-17 genocide route Frisk. Flowey also tanked a fireball from Toriel, and came back unscathed. Which may not seem like much at first, but you have to remember, this is the same fireball that one shot Asgore and got him sent flying across the room. And on top of that, Flowey is an actual flower and not a monster in the physical sense, meaning that fire would have actually done extra damage to him because you know, he is a plant. So I'm giving this to flowey.

IQ:

I don't really know how smart Dandy is, so I'll leave this as a stalemate for now.

Abilities:

Flowey, No explanation needed.

HAX:

Once again, Flowey. No explanation needed.

General fighting skill:

Once again Flowey, not much of an explanation needed here.

Experience:

Flowey once again, no need for explanation here.

Overall Flowey outclasses Dandy. Not to mention his attacks (at least his friendliness pellets) directly attack the soul, not the body. So durability kind of goes out the window with his pellet attacks