Navagon: Not sure why you'd want a version of the game with some really illogical design decisions left in place. BFG edition does a lot to improve on the game as well as provide some welcome extra content.
Fenixp: Basically, when it was released, the game has been (obviously) constructed around the way it's designed and BFG edition then slapped a bunch of mods and changed a bunch of things with no regard to how will these changes affect the original design. Like the design decisions developers have made or not, Doom 3 is a very tightly designed game - and removing the "Illogical" bits from the design doesn't make it a better game, quite the contrary.
I can understand that if you disliked Doom 3 originally, these changes might make you like it better - but that's kinda like slapping a sharpening filter on pixel art and say it's better because it's sharper. Sure, you might personally like it and that's fine, but the quality of the piece has just deteriorated. Doom 3 already allowed players to heavily modify it, you could apply the "sharpening filter" yourself - which is an option BFG edition removes entirely and pushes the modified vision on everybody.
The problem with your analogy is that your average piece of pixel art isn't in a constant state of change and growth over a five year period. Plenty of changes were made for personal preferential reasons over the course of its development. And let's not forget your analogy would require that it's the pixel artist returning to his own work and deciding that it would look better if it was sharper. Which is something they have every right to do and either you like the final work or you don't.
The flash light wasn't in the game during the first few years of development. Given the state the game was in back in 2002, which is to say fairly advanced, that means large sections of the game weren't designed with the flash light in mind at all. Yes, clearly there were sections added to make it more vital. But I don't think those sections play any worse at all without the separate flash light. They're a bit less clumsy. But I don't see that as a bad thing.
Also, early versions had radically differently balanced weapons. The rocket launcher could be used in close quarters without killing yourself, the pistol was weak as piss and the shotgun was closer to the Doom one.
My point being: these things have changed during the game's development and affected the way it plays. So whole sections of the game play differently in the original Doom 3 than they did when they were designed. The BFG edition could be seen as a continuation of that development. And while it could have done so much more. Especially to counter the fact that the lack of separate flash light made things easier, the changes aren't inherently negative. They just don't go quite far enough to rebalance the game properly.
Personally I would have preferred a more comprehensive rebalancing of the game. But what the hell. It plays well enough as it is.