I cannot agree on that. I always see my box busy at load XML stage while HD LED idle(my box is quite new, 8G RAM, run a 64bit OS, disable OS pagefile, so almost everything is cache in RAM after they're read once).
The point is they need to be read once, and that one time takes more time and it is happening during the xml reading stage.
One sign of complexity is dependancy: much more cross checking and step-on calculating are need in WoC than regular XML.
WoC adds much, much more flexibility to the game, in trade of increasing of complexity and overhead.
Your CPU is fast, you will not notice that, we are talking a few milliseconds here, I doubt it adds up to even one second. There also is not that much more checking necessary, here are the steps I expect are additional
- read MLF to determine order of reading actual definitions
- read actual definitions
- for each definition, check nothing whatsoever (over what CIV already checks) unless there are dependencies
- if there are dependencies, check that all dependencies are met (i.e. all definitions it depends on have already been read)
- if all have been read, everything is fine
- if one or more definitions are missing, discard this definition
That is it, actually that is next to nothing. It does not try to figure out a way to somehow merge all those definitions in the best possible way and juggle the dependencies while doing so, I agree that would be complex.
If you want to see how much of it is due to your HD, just unpak my FPKs and move them out of assets, then you will see how much time it takes to load small art files compared to large FPKs

This might be a rule of nature; but if the overhead can easely go beyond the endurance of a regular player, that could mean the project is going too far on flexibility side.
imo the real problem would be the unpaked art, which is why I still pak it (while the WoC rule is not to do so as it then cannot be removed if you do not use it).
As to the longer loading time, given that you load for a minute and play for an hour or more, the additional load time should not matter that much.