Modifications
The single most popular modification most owners make involves replacing the exhaust system and air filter with something less restrictive. When that happens airflow through the engine is increased and so a corresponding increase in fuel is required.
Some EFI systems can cope with minor, (and I have to stress the word minor here) changes in airflow. Most can't, so they have to be coerced into providing more fuel. While there are some ECUs with replaceable chips, those are mainly found on older sportbikes, so we'll leave any discussion of them to the guys who own them. Likewise, reflashing a computer, or writing custom programs isn't for the faint hearted so I'd leave that option to the pros, particularly the ones with lots of experience and a dyno.
If you're planning on doing it yourself, the simplest and most cost effective way to modify the fuel map is by installing an add-on fuel module, or "cheater."
There are two types of cheaters on the market. The first intercepts the sensor signals and then modifies them, before passing them onto the ECU. Typically they'll tell the ECU that the coolant temperature is cooler than it is, so the ECU extends the injector pulse width, resulting in a richer mixture. The second, which is far less common, changes the injector pulse width after it leaves the ECU, leaving the sensor signals as they were.
The boxes are normally preprogrammed for a given application, and can be fine-tuned via trimmer screws. A few can even accept custom programs, and there's a couple that can be programmed on the fly using push buttons. Installation is generally straightforward, in most cases installing a box requires a lot less work than rejetting a carburetor and most are plug and play applications so you're good to go out of the box.
Of course, if you plan on going completely nuts, as far as building a high performance bike that is, the aftermarket will be only too happy to supply you with everything from oversize fuel injectors to new ECU's.
Down the Road
Despite their current level of sophistication, the existing state of the art in EFI systems has barely scratched the surface. As systems become cheaper and more technically advanced, and the government becomes more involved expect to see easier to access on board diagnostics, similar to the OBD II systems that all passenger cars now use. I think we'll also see things like launch and traction control become more common, at least on high end/high horsepower machines.
Already some of the more powerful bikes, the Suzuki B-King comes to mind, are equipped with alternate power curve mappings, one setting for rainy days, another for dry so expect to see more of them over time. Down the road, I'd also look for things like variable valve timing, especially on top of the line sport touring bikes, and more mundane technology like acoustical anti-knock sensors that sense detonation as it occurs, and adjust the fuel and ignition timing curves to eliminate it. All of this and more is already available in the automotive world so it's only a matter of time before it trickles down to even the lowest echelon of motorcycling.