When I purchased my new Heritage in 2004, I really wanted a Carbed bike, because they are so easy to do mods on. I fell in love with the color of the bike I have, and did not want to wait 6 weeks to get it in a Carbed model. Since then I have done a 95-103 and 107 Stroker installation on it. Including S&S High Output oil pump, heavy duty starter and compression releases, oil cooler, 57mm EFI racing throttle body, and several sets of exhaust systems to see which ones produced the best HP/Torque curve. BELIEVE ME, when I say, with a carbed bike it would have been a breeze to Dyno tune the bike, you install the mods and re jet the carb. This is compared to installing a Power Commander, and having to tune that every time a new fairly substantial mod was done, as EFI is not to forgiving if run in an un tuned state. You just don't whip out the trusty screwdriver and re adjust the jets.
On the other hand, when the EFI is tuned to perfection, it is unbeatable in reliability, and NEVER gives you a problem after sitting all winter in the garage. In the Spring you just hit the starter and off it goes. My bike is Dynoed out at 115 HP and 121 FPT, but it would have been a lot cheaper and easier if it had a carburetor on it instead of EFI.
I don't think that carbed bikes will be around within the next decade at most. So if you plan on doing a lot of engine modifications go with the carbed engine. If you want to jump on the bike in Heat or freezing weather and have it start right up without screwing around with a choke etc, EFI is where it is at.