Ill answer to the best of my knowledge.
1. I was able to get Chartboost ads working perfectly with XDK using Cranberry's cordova plugins. Another option for ads is the Appodeal C2 plugin. It works great by itself, but as soon as I tried to add plugins for other functionality (Cranberry analytics) I got build errors so I swapped it for Cranberry Chartboost and that way I was able to get both ads and analytics both working in my game at once. I haven't tried iAP, (cranberry or official plugin).
2. From what I understand from reading through the forums, the general consensus is that the the official C2 plugins for AdMob and GooglePlay are outdated and not recommended. Again IAP Im not sure I havent tried yet.
3. Working with XDK, you will need to use the Cranberry Cordova plugins for Ads and Google Analytics. Im not sure about Cranberry iAP. Important to note, Cranberry's GooglePlay plugin doesn't seem to work with XDK. At least I was unable to get it working.
4. After failing with Cranberry Google Play on XDK I swapped to Cocoon.io. I was able to get Cranberry's Google Analytics working quickly. I discovered that Cocoon actually has their own plugins for ads and for GooglePlay. I was able to get the Cocoon GooglePlay plugin working after about a day of playing with it (now its working very well). Next I will attempt to use the Appodeal ads plugin with Cocoon, if that fails Ill try Cocoon's ads plugins (they have options for Chartboost, AdMob and a couple others). If that fails Ill use Cranberry's Chartboost plugin, and if that fails I'll kill myself.
-I would quite happily recommend XDK by itself. I was able to get great performance with my game on XDK (on Android and iOS). The problem is, as far as I know, we are reliant on Cranberry's plugins. He doesn't provide any support what so ever, so if you can't get it working yourself you're stuck. So While XDK itself is great... as soon as you need ads, analytics, Google Play, you are forced to rely on 3rd party plugins that are unsupported. I got analytics and ads working, but hit a wall with Google Play. I posted about it on the XDK forum here.
-I like it that Cocoon has their own up-to-date plugins for essential functions like ads and GooglePlay. I would much rather use theirs than unsupported options.
-When building on Cocoon you have a couple options to choose from under settings>webview engine: (webview, webview+, canvas+). I get great performance (equal to XDK) using webview or webview+. But I get terrible performance with canvas+.
-It's possible I'll still use XDK for iOS **if** I can get GameCenter working on XDK... havent tried yet.
This is a summary of my experience from the last fortnight. Hope its useful to you.