Porting to 1.6 when a mod works with 1.5 is indeed extremely easy. I tested this with RTRPE a while back: all you have to do is install the game over BI and delete/rename your bi subfolder. Then run the game using the RomeTW-BI.exe file and it works just fine. The game also creates another bi subfolder with a new preferences folder and such, and you can place any 1.6-specific files in the bi\data folder so you can still use the 1.5 exe to run the game normally if you want.
There is also another option, where you can run a simple .bat file before installing a 1.5 mod over BI that changes the file structure to allow the mod to be run directly with the BI exe.
Both methods seem to be extremely stable; I've not had any problems using RTRPE with the BI exe at all. There are no huge differences between using the two exes, though, I *think* there's a few minor tweaks to the AI and the AI factions seem more capable of using the prefers_naval_invasions feature in 1.6 than 1.5.
So IMHO, using the BI executable for EB should only be a concern after a 1.5-compatible version is released.
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