I'm planning to use the enterprise edition for the production server, but it will take a few months to get the custom development ready, so my question is if we develop the code based on the community edition, will it be a problem to migrate to enterprise edition later?
Enterprise has 41 modules that are separate from the community edition code base. These include modules which cover areas such as:
- Page Caching
- Reward Points
So while the core magento Mage_* functionality should be expected to be the same, depending on what functionality you are looking to make use of it may very well be that the Enterprise functionality replaces or augments how it is in use.
If you plan to build on Enterprise, then you would be best getting the Enterprise License setup, and develop the site on that rather than build it blindly and hope that you do not run into problems.