As a result of sp. atk/def not being used, all the special type pokemon are at the bottom of the food chain, and the physical pokemon are at the top.

To level the playing field without having to change the core mechanics of the game, you could either have the stat values of pokemon be atk+sp.atk, or (atk+sp.atk)/2 to keep the numbers a little lower.

Can you explain this to me a little bit further?
The special Pokémon and physical Pokémon refers to which type of Pokémon?
I don’t see how it effects the types of battles that are in this game, I mean, the battles are designed to be one by specific types (ghost, dark, steel, etc) and that means physical and special of said types have equal chances of winning said fights too, right?

Alright, let me use the special type pokemon Alakazam as an example.

This is what Alakazam's stats look like:

HP 55
Atk 50
Def 45
Sp. Atk 135
Sp. Def 85
Speed 120
Total stats: 490

But in Dusk, those special atk/def stats are ignored, so Alakazam's total stats drop all the way down to 270. Now if it was a physical pokemon instead and those stats were swapped, it's total would go up to 395. This clearly favours physical pokemon.

That is, if the stats are taken into consideration in battles at all.

I don’t think stats are considered at all, I think it’s all about typing with battles in this game. Because, it didn’t matter if you’re using a special or a physical stat pokemon from what I’ve noticed, it just mattered if you’re using the right type (dark, psychic, fighting, etc) for the trainer you’re fighting.

It doesn't make sense that stats wouldn't be used at all, so I did a small test and stats are most definitely used in battles, I'm 100% certain.

Used a level 224 Absol (130 Atk) to attack a level 105 Clefable with Scratch. Damage was in the 400-700 range.
Used a level 224 Chansey (5 Atk) to attack the same level 105 Clefable with Scratch. Damage was in the 15-40 range.

So yes, the stats are definitely significant.