Hi Brian, the main thing is to remember that the M in Moodle stands for "Modular" - make sure that any modifications are contained in a module - the API lets you do quite extensive things with modules and/or blocks.
If you are starting now, I would suggest budgeting for development against both 1.9.x and 2.0 for the most 'future proof' results.
It is also always best with any software development to plan for ~ 20%-30% of the development costs/year for upgrades- not just Moodle may change over the coming years - Flash itself has changed dramatically since I started using FutureSplash back in 1995, & Moodle has changed a bit over the years as well.
In any event, beware any code changes that modify core Moodle code -these should be looked at especially closely, as these are the sort of changes that are most difficult to support in new versions. Sometimes a core modification is the only way to get what you need done, but as with dynamite, there is usually a better way.