While 2.6 and 3.X look very similar, theres lots of incremental work that has been done to improve the system. The main page "portal" is now Iframe'd and you have the option to add other applications Iframes to that portal.
The device credential repository (DCR) now is used by everything and very tightly integrated. DCRcli is now actually useful.
The trouble shooting assistant queries all the applications for everything they know about a device (campus, IPM, RME, DFM,syslog, reachability from the management station and presents it in a single pane.
IPM is completely re-written and worth the price alone if you do any IPSLA configurations as you can deploy multitudes of probes using a single set up run, no longer is it one to one. The java clients in IPM are history... the graphing engine has been replaced and looks about 2,000% better. You can support up to 5,000 probes (with the December update) per instance of IPM.
The discovery engine now resides in Common services and can now employ OSPF and BGP in finding new devices.
Now the pricing changed a bit... theres no longer sku's for 50, 100, 300 , 1000 and unlimited. The top size is 10,000 devices for a cluster.
Its more reasonable the more devices you toss at it as it can handle more for less money that any competing product.
Its much better than when I began using its earlier incarnation, Ciscoworks Blue for IBM.