While MailPoet has put some effort into its configuration on MultiSite, I think there is some more room for big improvement. (Note that I've written about the topic before (https://wordpress.org/support/topic/suggestion-some-multisite-improvements?replies=1#post-5720905), but these are additional suggestions - though all those are still very valid.)
1) Stop storing options in an base64_encoded fashion.
As far as I can tell, there is no good reason to store them like this, and it makes it much more difficult to work with. (Of course, if there IS a good reason for storing them like this, please let me know what it is!)
2) Move 'Archive page Shortcode' out of "Geeky options". It's really not that 'geeky', and is a pretty important thing to know how to display!
In MultiSite environments, the following are all things that I think should be removed from Site Administrators and reserved for Network Administrators. (Optionally, you could let Network Admins decide whether or not Site Admins can control them.)
3) Roles and Permissions
I don't believe that Site Admins should have this much control over roles land permissions, and some of them are downright dangerous to begin with. (Why would you want to let Subscribers create newsletters??)
4) Share Anonymous Data
This makes much more sense to be in the hands of the Network Administrator than Site Administrators.
This is overly confusing for most Site Admins, and should probably be left to Network Admins. At a minimum, I'd strongly recommend adding some text along the lines of "If you don't know what this is, just leave it at UTF-8"
6) Debug Mode
Another thing that should be left for Network Admins. Site Admins shouldn't be able to display PHP errors or SQL queries.
7) Premium menu and Add-ons tab
In a MultiSite environment, Site Administrators can't install plugins, so why are these options displayed? If a Site Admin clicks a link to install one of these, they'll just receive the message "You do not have sufficient permissions to install plugins on this site." these should just be hidden from Site Admins.
Thanks for listening - and let me know if you have any thoughts on these you'd like to share or discuss.