Take the 'B' kit, as it contains the PSoC3 production silicon. PSoC5 is still on ES1 AFAIK, there isn't even ES2 available.
But the 001 has much more ports available. I agree that the 050 is better if you want best analog performance, but I easily maxed out its available ports (as some are already in use). And even the 050 has no newer PSoC5 silicon on it.
Yes, there are more ports on the -001 kit, but some I/O pins are shared between ports ,
so you need to be mindful of what you are using. Also, the best Analog ports P0[7-0]
are used for the CapSense buttons, so you will get extra capacitive loading on those lines,