@Mantis I'm sorry it's not working out for you, you may be right and maybe you bought the wrong pedal and an ES-5 or 8 (or the mastermind or whatever) may be better for you?
I'm still in the honeymoon period but I have a few differences with your setup/opinion:
1) I don't go in the loop, just in front
2) I don't mind the global EQ. Depending on where I play (venue, microphone etc) I tweak my settings and this just makes it easy for me
3) it feels like you had a very clear expectation of how navigation should work. I didn't and it works ok, I can get patches done. The desktop software will be out in a couple of weeks.
4) I'm ok with the trade off when I want to have a looper and multi effects in one for $400. I sold my EHX Silencer. Is the gate on the MS-3 great? No, but it will do the job, maybe I get to make it work better as I use it.
5) I assumed that with the buffer it was going to alter my tone but I'm fine with how I can tweak it back with the global EQ.
6) Most of my tone comes from my amp and the DMM in front. Apart from the reverb (which I may get something after the ES-3 for) I don't really need a ton of the effects. It's just a nice have that saves me from having pedals I rarely use.
You may make somebody here happy if you flip it
Btw you may want to ask your questions here
https://www.thegearpage.net/board/index.php?threads/boss-ms-3.1832750/page-18
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