I think there is some confusion here.. includes are useful for when you have a chunk of code that needs to be called in every page..
For instance consider a top menu navigation system..
(pardon the pun, but no 'ifs' about it.. you would be best to use an include (or require). In the event you need to make any modifications, you simply modify the include / require file, and the changes are propogated site wide. This has nothing to do with 1 big file vs include.
You can have 1 big file or an equally big file using a smaller base file with some includes. It's the 'update-able modularity' aspect of an include that should be taken into consideration, as this is what it's used for.
Cheers,
NRG