Pat, in general, yes, there will be some capabilities of Skuid-on-Salesforce that will not be present on Skuid Native, but you’ll see that we have tried to keep the feature set and functionality as close as is possible and reasonable.
Regarding your specific questions:
1. Right now, Lightning Components are not available in Skuid Native — no plans right now to change this.
2. Invocable Apex — also not available right now, but may very well change in the future.
3. Salesforce Buttons — no plans to add this, doesn’t really make sense on Skuid Native.
4. Global Merge Variables — virtually all Global Merge Variables available in Skuid-on-Salesforce have direct correspondents in Skuid Native. $Label, $User, $Site.CurrentSiteUrl, $Site.Prefix, etc. all work in Skuid Native.
There are of course other capabilities that you did not mention, such as calling Visualforce Remoting and executing Apex, which naturally don’t make sense on Skuid Native because it’s not on Salesforce anymore.
But, there are things that you have to do on Skuid-on-Salesforce right now which are much easier on Skuid-Native.
For example, deployment of Pages.
In, Skuid Native, you have Apps and Routes. Routes basically let you say, “when Users go to this URL, show them this Page”, and Apps are bundles / groupings of Routes, accomplishing much of the functionality of Salesforce Communities and Apps all in one. Apps and Routes are so simple to use, you’ll probably catch yourself thinking “Wait, that’s it?” And yes, it is that simple. No Visualforce Override pages, no overriding of Object Actions, no Page Assignments ---- just Routes.