I agree, this is one unholy mess.
You have to be conscious of what has created what, because Apple gives no clues, all files are .pages files.
None of the Pages versions can open later version files, even down to the minor Version 5 upgrades and Apple has switched and changed all the formats multiple times. All of which is compounded by the incompatibilities with all the OSes, the different versions of OSX and iOS.
Pages '09 is the most compatible, it will run on everything from OSX 10.6.8 to OSX 10.10.2 so is the version to go for. It also has the most features and greatest ease of use, so if you choose one format this is the sensible one. The only problem is Apple will eventually cut it loose.
Pages 5 is useless IMHO as it has so few features, has an extremely clumsy and ill thought out User Interface and headed for exactly the same scrap heap everything else Apple heads to. In short: Avoid!
Use Pages '09 v4.3 for now and Export any Pages 5 files back, until something better (not from Apple) comes along, which should be soon.
Meanwhile let Apple know what you think (and that you still do) by rating/reviewing Pages 5.5.1 in the App Store.
Peter