Performance is pretty much the same - functionally not quite. The 5000 has its own remotes that won't work anything else, and the multiroom link system is also incompatible. Connections are about the same though; for example AUX & CD are still combined on the Beomaster 5500, whereas on 6500 they were separated into different inputs.

Is the 5000 capable of driving a multiroom MCL2 system?

No - from what I understand, it used a completely different multiroom link system (MCL82 as shared with Beocenter 7xxx - hopefully someone will correct if I'm talking BS here).

But you have to be careful with BS 5500 as well. Earlier versions of the Beomaster 5500 need a software update to work in a multiroom setup, see this thread.

Both points quite true - though the main problem with the 5500 is that it may not like the later two way controllers (BL5000/7000). With the MCP5500 it is fine. I use a 5500 daily as the huge advantage it has over the 6500 and 7000 is the amount of connections. As well as DIN it also has a full set of RCA plugs which means it is ideal for connecting to computers and iPods etc.