I don’t know if Logos can do anything about it, but the “Replace with Passage” feature no longer works with the new Pages 5.0.
I noticed that Apple stripped a lot of the scripting language out of Pages, so I am thinking that Logos won’t be able to fix this—but I am hoping against hope that they can!
On the bright side, the new Pages supports Hebrew. I haven't tested to see how well it works, but it's much better than the old version.
It also does not bloat the file size of the document anymore when passing the document back and forth between a Mac and iPad via the iCloud. The file sizes were always 5.6 mb when I did this, now they are a more normal 100-200 kb.
Also of note is that you can now highlight your documents both on the Mac and the iPad (albeit only in one color). This will help me since I preach from Pages on the iPad.