Personally, I just decide on what I think the character would use - depending on what sort of person they are - a hulking great barbarian might go for something big & heavy like a maul or great axe, while a sneaky rogue might prefer something small like a pair of daggers.
I suppose it all depends on whether you see the game as a system of numbers, or a means to roleplay a character with their own personality and approach to the world.
Back my P&P days, quite often we'd be looking for whatever equipment matched the lead figure we'd painted up to play the character, while in NWN1 it was sometimes a case of basing the character & their equipment on the portrait we'd found.

NWN2-wise, although weapon length & speed isn't modeled, there are a couple of differences to be aware of:
Light weapons can be more easily dual wielded
Single handed weapons allow the use of a shield, increasing your armour class
Double handed weapons do quite a bit more damage, especially if your character has high strength
Once you get into the realms of bonuses to damage from the various magic weapons you can pick up, the initial weapon base damage doesn't really matter that much any more - the difference in base damage between a dagger and say a long sword is pretty much minimised when they've got all sorts of magical extras, like d6 fire damage, +2 weapon, etc.
So, specialise in whatever you like, depending on how you want to play the game, although as Arkalezth mentioned above, in some modules available, some weapons are more common than others - you won't find many characters specialised in Scythe, as they'll probably never find any decent ones in the shops.

Also, I've not seen that many characters using scimitars, possibly because they look so horrid in game!
Cly.