The strategy part of the Pokemon games is like a completely separate aspect of them. While LC (and a lot of other hacks) puts emphasis on the RPG part (sprites, maps, events) the strategy part is sometimes suffers some degree of compromise (albeit completely unintentional).
The phys/spec split, however, puts a different twist into the game, not necessarily harming it. Some pokemon benefit from it, while others are hindered. Typhlosion, for instance, is quite bad now, as it can no longer utilize a special Thunderpunch for coverage. On the other hand, Feraligatr (which is my starter in LC) is vastly improved, now possessing a STAB physical Waterfall and getting very good coverage with only two physical moves (Waterfall and Return/Double Edge). Plus it gets physical Ice Punch, Bite, Crunch, etc for more super effective coverage.
Another example would be Dragon Claw. As it's now physical, Dragonite and Salamence can be much more threatening, not having to rely on HP Flying. Latios, on the other hand, is crippled and has to rely on either HP Dragon or Dragonbreathe.
As for Hyper Beam, that is pretty much an overrated move, considering Return hits hard enough, has just as good distribution, doesn't require recharge and it is still physical.
So, IMO the split should stay as it doesn't necessarily unbalance the game too much. Plus its implementation is now near perfect and it makes the gameplay more complex.
