The ECU is easy to remove:
http://www.yamahasupertenere.com/index.php?topic=7356.0
I have also posted here with pictures:
http://www.adventurebikers.net/forum/index.php?topic=1317.0
And a similar service is offered by CJS racing at £199:
http://www.yamahasupertenere.com/index.php?topic=14523
CJS also offer ride-in / ride-out if you are not comfortable removing your own ECU or a full custom mapping service which is a full day of customised dyno setup, they should also be able to sort out low rpm fuelling problems on bikes with Full Exhaust Systems, which I do not think the Flashtune flashes can.
IMO if all you want to do is lose the restrictions any flash out there will do that well, personally I think the ECU-U flash makes the throttle a bit too aggressive (and I have fitted quicker action throttles to bikes in the past) and are expensive at £350.
If you want to get the bike 100% spot on, or have done other mods such as Exhaust system / air filter changes it is much better to get the bike setup on a dyno.
At least there are finally some good value options in the UK.