You can replace nUI's default aura bars with aura buttons by downloading the "Aura Buttons" plugin from the "nUI: Unit Frame Panels" section at
http://files.nUIaddon.com ... that should fix the one issue you raised in the first section.
You can also download the "Stats" plugin from the "nUI: Info Panel Plugins" section at
http://files.nUIaddon.com and that will cause your Omen3 and Recount windows to auto switch between Omen in combat and Recount out of combat. There's also a "Dual Stats" plugin that displays both Omen and Recount side by side in the same info panel. Another option is to replace Omen3 and Recount with Skada which does the job of both of those addons and does not require a plugin.
The FPS issue is a known issue affecting some players (a lot of players) and is at the top of the list to be addressed in nUI6. Likewise, nUI6+ will be fully customizable via a GUI configuration system.
As you've already noted, nUI does not include a Boss mod functionality. However, it is compatible with all boss mods out there, so it is as you say as simple as installing the Boss mod you like and positioning it as you prefer and you're done. I do not intend to build boss mod functionality into nUI ever... no point really and it's well beyond what the design intention of nUI is.
PallyPower and Zomgbuffs are both things I'll have a look at.