If you like the way the bike runs now, there are no known issues with the fuel injected Road Stars or Roadliners. Some minor things to keep an eye on, but no real design issues.
If you only put an aftermarket exhaust on it, you dont really have to retune the ECM. If you change the intake then yes, get the ECM re-flashed with a modified fuel map to give it more fuel.
There is a lot to be said for a fully stock Vstar bike. The engineers at Yamaha really knew what they were doing, and a stock bike will easily go 100,000 miles without engine problems.
If you want to make the bike look different, there is no limit to what you can do to it.