Why can't we purchase chain by the meter, in any length, instead of in fixed lengths? Then the chain could be cut to the exact length required, unlike current situation of throwing away several links. This might not be beneficial for end users, but what about large bike shops or even OEM bike manufacturers.
They do. Connex (Wipperman) sells bulk chain, as shown by this link, and these people also buy it by the spool. This is likely what bike manufacturers do, and I've seen it in a bike shop or two. I'm sure you can also get it at some place like McMaster-Carr or Grainger if you ask for ANSI #40 roller chain with the appropriate width (possibly by special order).
The only bikes which use bigger chains than a standard chains are custom, longtails, tandems or recumbents -- its just more convenient for 99.999% of the people to just get a standard length chain [and many of these are pretty close to just taking multiple chains joined together]. As for the few extra links "waste", they come in useful sometimes when you need to do a repair. And in net, its probably cheaper to just pick up a little plastic box which has a slightly larger chain than going to the LBS and asking the girl to break the chain to the exact number of links you need (remember, she needs to get paid and do the daunting task of counting/comparing the # of links in your old chain to the new chain provided you actually brought the old chain in. if you didn't do that, she has to assume you didn't muck up the # of links in the chain and you wont complain if your new chain ends up too short). And its quicker.