Couple of years back I was handling a document conversion project for a well known multinational. There were two main obstacles that we had to face.
1. The main document that we had to scan was in a non standard size. It was a bit longer than an A3 paper. This prevented us from using most of our scanners, since they were not capable of scanning papers longer than A3. Among all what we had, the only scanner capable of this at that time was the good old Kodak - I 260. Even for that we had to add additional RAM. (At present the problem is not that significant since there are several models of scanners that support scanning of extra-long documents.).
What we can learn from this is that it would be very much easy and cheaper to scan a standard size document than a non-standard size. The scanners are designed having considering the standard paper sizes (ISO as well as US sizes). More than that, this is a main factor upon which the price of a scanner depends on. As an example a scanner that can scan A3 size documents will cost around 4-5 times of a scanner that can scan only up to A4 or legal. So my personal opinion is that it is always good to keep your documents at A4 or legal size. This also helps a lot in the handling as well as storage of documents. Having non standard size documents will make it more difficult to file, store and even copy a document.
2. The main document was an application form which had all the filled in information in one side and the applicant's signature on the other side. That was because the second side was full of all the terms and conditions under which the customer had to place the signature. Since the signature was required to capture we had to scan both sides of the page.
If the signature was on the same side along with the other details then we could have scanned only that side of the page. This would have reduced the cost of conversion by 50% , and reduced the project duration at least by 20-30%. Not only that we would have reduced the storage and bandwidth requirements by about 30%. So this is a good example why you need to consider about the layout of the documents.
These are just two examples of how the size and the layout of documents will matter in your ECM activities.