This is a tough one. Funky cars are in increasingly short supply. Aside from the Mini and the Soul few have sold well, so most manufacturers are again playing it safe. On top of this, manual transmissions are increasingly restricted to lower trim levels and the smallest engine, when they are offered at all. In some cases you can get a manual transmission and AWD, but not together (e.g. the first generation Audi A3, the Mazda CX-5, and the VW Tiguan).
The Buick Encore is quiet and luxurious, but no manual transmission is available.
The 2014 Soul is far better than the first generation. But as you note, no manual except on the base model (increasingly common) and no AWD at all.
The vehicle that best checks off all your boxes is the Mini Countryman. Some people do have bad experiences with Minis, but many others don't. If it really does suit your needs much better than anything else, it's probably worth the risk.
Next closest is probably the Subaru Impreza WRX hatchback. The 2008s and 2009s have had some engine issues, but newer than that should be okay. If the WRX is much more powerful than you need, then check out the regular Impreza.
With both the Countryman and the WRX, check that they have enough cargo space.