I just finished a mobile game with ads & IAP recently with C2, it was compiled with Cocoon.io Canvas+ for iOS and Android, it was pretty straight forward, no more work than putting an ad sdk in past Unity or GM:S games I have made. I used the Verstala Heyzap plugin found here , I am currently using Admob, UnityAds, Vungle and Heyzap video and reward ads in the game. The plugin is extremely easy to use, comes with good documentation for set up also.
I ran into a few hiccups getting compiler errors but literally 99% of the time it was because I messed up with the config.xml in Cocoon. A few tips for things I did that made everything work.
1. When exporting from C2 make sure Minify script if unchecked and PNG recompression is set to "None"
2. When zipping your C2 project for upload to Cocoon do not include the config.xml file or the intelxdk.config.additions.xml file in the zip, I manually add the plugins myself in Cocoon.
3. Set Multidex enabled to "Yes" for Android builds.
4. Make sure every plugin you are using in C2 is also included in the Cocoon.xml file.
5. Make sure any plugins you are getting from Github have the ".git" appended to the end of the URL in the Cocoon config.xml file(See example configs below).
6. Check in Cocoon under Installed plugins and make sure Cocoon didn't add any of the "Whitelist" plugins to your project, I got a black screen everytime one of these plugins where included.
Example iOS config.xml with Verstala Hepzap plugin, Cranberry Game Center leaderboards, EddyVerbruggen Social Sharing Plugin and Cocoon IAP plugin.