It may take a bit longer to create themes for the iPhone 6 Plus (kind of how it took longer to get themes for the iPad ... if at all).
The icons on the Plus have a different size and naming protocol than on the "regular" iPhone 6. So, a developer has to create at least two different icons for every app he/she themes.
So, this may (will) take more time to create and some developers may end up theming for only one device - which is most likely the one they own.
The same will go for tweaks. Although, from what I can tell, most tweaks that work on the regular iPhone 6 also work on the iPhone 6 Plus, consideration will have to be made for the differences. Essentially, although they are both iPhones, they really are two different products.
So, yeah, I'd expect some delay in creating tweaks and themes for the iPhone 6 Plus. Themes more so than tweaks, but still.
Marilyn