I don't have any experience with in-wall speakers so I can't make suggestions.
There are several good satellite systems, all wall mountable and all would be a significant improvement over the Bose ...
- Paradigm MilleniaOne 5.0 $1000 (also comes in white)
- Cambridge Audio Minx 5.0 $730 (Min21 x 3 LCR, Min11 x2 surrounds, also come in white, $75 extra for the wall mounts or table stands)
- KEF KHT 3005 series 5.1 $1100 (only comes in black)
Focal also has a couple of superb satellite systems (Dome, Bird) but they are considerably more expensive than the Bose.
Re Subs: I'd recommend not getting the sub that "comes with" the satellite speaker 5.1 systems (you can purchase the satellites as 5.0).
- The Go-To budget HT sub most often recommended in the forums is the Klipsch RW12D for $300 give or take depending on a sale. If you go with in walls it would be fine. IMO it's a bit too sloppy to be optimal for use with satellite speakers. Since they're smaller satellite speakers need a higher crossover. This means the sub is covering more of the upper bass and lower mid-range frequencies so you want a sub that's very tight, accurate and detailed, esp. in it's upper register.
- There are several ID sub manufacturers with excellent subs in the $550 to $650 range - in no particular order SVS, Rythmik, HSU, and Outlaw. I happen to have the SVS SB12-NSD and it's excellent (and it's uniquely small, which may be good for your WAF), but subs from any of those ID companies would work equally well