Magico S5 Speaker - SET UP ADVICE PLEASE - Tow-In - Etc.

Get the grills off the speakers!!! All Fixed. My S3 are different speakers with grills on and off. That's why they are optional. 

Have you tried the Cardas speaker positioning? 
http://www.cardas.com/speaker_placement.php
The speakers look like they should be pulled out, from the front wall more?
You've got a coffee table in front of the listening sofa along with the TV/rack between the speakers. Room treatment?

 Game over, if you're expecting "high performance" sonics. At least  that's what some of those "audio experts" might mention, looking at the pics?

It appears the system is in a "living space" so WAF,aesthetics,etc also limiting ultimate SQ?

With all that nice gear,speakers and doodads, it's a shame you're not satisfied.
And I see suggestions for MORE doodads! 

Good luck.

Anyway dont forget that Magico's Love A class but over 50W ;)

Glad to see you're making positive forward progress. 

As I said earlier, beryllium tweeters are touchy.  I've now had three different pairs of speakers with those tweeters and when not implemented perfect, they're a little too exciting for their own good (which was the case on my older Focal Scalas). 

One of the things all beryllium tweeters need is clean power - for some reason they are very sensitive to clean power, much more so than other types of tweeters.

The pics confirm my fears about your room. 

If you don't treat your room (which looks to be too small for those speakers), you probably will never be fully happy with those tweeters.  It's just the nature of the beast.  That TV needs to be covered up when listening with a panel and those windows behind the speakers as well (look into moveable panels that you can keep elsewhere and then put up when needed).  Another thing you really need is an absorptive area rug, what I see doesn't look like it does much.  The table needs to go.  That leather couch is also an issue - you want absorptive cloth.  You also really need to treat that wall right behind the listening position.  Finally, if those speakers are on a typical US floor, then you've got to get some isolators as you need either direct coupling to concrete (which is what I have) or suspension.

Having said all that, you're also sitting WAY TOO CLOSE to the speakers if they have beryllium tweeters.  Also, my experience is that with beryllium tweeters you really need a system whereby you can shelve the output slightly up or down to also account for your room (which is one thing I've found that's an amazing option on Focals - that 1db up or down can make a huge difference).

Two things to add if not already mentioned. I too have an M1 and have never found it to be anything other than a wonderfully musical device and going direct to amp sounds great. It’s true that you might need to lower the output voltage which is not very hard to do. don’t even consider ditching the M1 as it’s not a problem but an asset. 
The other thing I might consider is a $300 pair of GIK free standing panels(2’w x 5’ t) to place at first reflection point. Easy to move around and will definitely dampen any nasty/hot  first reflection points. I actually prefer mine a little further down the length of the room. Point being you can find your sweet spot. 
Just my humble opinion and best wishes.