Steve,
A few thoughts for you.
First regarding version, right now for new production sites, I am still sticking with 4.9.2 as it is proven and stable. I do have some clients with production sites on 5.x but they needed some of the specific features of that version.
Secondly, regarding needed modules, for subscriptions, I would strongly recommend looking at either Inventua or Ventrian for subscription modules, both are easy to setup, and great to use.
.NET 3.5 support works with 4.8.0 and later from a full solution integration, but otherwise, the individual modules control it, so it isn't a big deal at all.
THe Microsoft Chart controls can work in it, I am using them for a series of tutorials and examples that I am preparing. They work awesome! I don't know of any publicly available modules though that use them.
As for sites/resources for developers.
1.) It wouldn't be right for me to not recommend my book Professional DotNetNuke Module Programming
2.) I have quite a few articles also posted on my site http://www.mitchelsellers.com
3.) Michael Washington also has a great number of resources.