When you close down Workspace Studio it will remember the settings for each instance of the gadgets including the SNMP Real Time Graph. There seems to be a bug when running SNMP Real Time Graph outside of Workspace Studio. It should remember the settings but that does not appear to work correctly at this time. If you open up a support ticket and reference this thread it will help us to get a fix for this prioritized.
As far as all of the graphing options being available we provided the most common options. Make sure you check out the general settings tab in the settings screen. When we updated the SNMP Real Time for IPv6 we implemented it with newer technologies as the existing implementation platform was becoming dated. It was not efficient or desirable to make the new version look just like the old one. If you would, let us know which options are missing that you find useful that don't have an acceptable current counter-part and we'll look into how best to handle that.