I agree with VC. Personally, I have nothing against ROM hacking, other than ROMs being illegal. Also, hacks have features which would be hard or impossible to have in a game. Off the top of my head, attack animations (making over 300 from scratch would take forever), ability to play on actual consoles (either through flash carts or the emulator for the PSP), and the ability to link with the official games.
But I'm going with game making, just because of the sheer freedom available. When you make a game from scratch, you have infinite possibilities. There are no limits to how many Pokémon you can insert, no 16-colour limit for sprites, no tileset limitations. But that's not it - not the main reason.
The main reason, at least for me, is that unlike hacks, which are stuck with the systems already present in the ROM, game makers can modify and add to the underlying mechanics as much as they want. In my own game alone, there is the physical/special split, an improved D/P style Pokédex, much more info on the summary screen, improved stat boxes in battle, a 'shortcut' pocket in the bag, the ability to change the trainer's clothes, expansive maps (64x64 tiles) 4 times the size of D/Ps (32x32) and 10 times the size of R/S/E's (20x20), and a completely new menu system (details coming soon :P) with a way to quickly change the order of your team. Not to mention all the D/P Pokémon, moves, abilities and items, as well as tons of new ones. In other games, I've seen higher resolutions, 5 regions, and online play. None of these I have ever seen in a hack.
Oh, and it is much easier to do stuff, too. What you call 'scripting' here, we call eventing. From what I've seen, eventing is a lot easier than scripting, but with more commands available. Also, adding a new Pokémon or trainer is as simple as adding some stats into a text file, and putting the sprite into the right folder. New moves, abilities and items are also easy to insert with a bit of scripting knowledge (not hack scripting - we're talking about programming languages here). And mapping also seems a lot simpler, with multiple layers, among other things.
All in all, I like game making more than hacking, due to the huge amounts of freedom not present in hacks.