On Beocentral they mention that the 6500 beomaster amp was somewhat ill conceived.

Why is this and is the Beomaster 5500 the better amp?

I think that to all intents and purposes the 5500/6500/7000 amps are exactly the same. The slightly more capable one is the 5000, so if you want to hear a difference, try one vs the later series. 

...or you could get a 6000 or 8000 to truly hear what a good amp sounds like :)

Not a lot in it - the 6500 has Powerlink sockets, the 5500 has lots of RCA plugs as well as 7 pin DIN. The 6500 will also work with the Beolink 7000 which the 5500 does not on the whole. I have both a 5500 and a 7000 and use the 5500.