My opinion is it depends.
My main gigger is the GC. You can't beat the flexibility and the ability to make it sound exactly like what you want it to. Plus the piezo isn't something you can really get on the Morse. If you feel you need more strat-ish or Tele sounds, you get a wide variety of these that you don't get with the Morse models. It's criminal how much the GC's are under-rated.
I really dig the Y2D though. Have to say I much prefer it over the std Morse. I can't get myself to adapt to the pickup switching of the old Morse so it's primarily a studio axe. The Y2D switching is much improved for people like me but I still have trouble getting theh 3 and 4 positions backwards in my head when performing.
The Y2D is much heavier, better looking, and got a much meatier sound than the old Morse. It's a VERY flexible axe in terms of tone, but you can't get more flexible than a gamechanger.
Both the Morse's do single coil stuff well but I find the GC covers a lot more single coil territoy well (for example, lower output stuff with a neck pick; single coil bridge; or the lower output in between sounds. GC does these really well).
A lot of people on this board are very much into their maple tops and I love the top on the Y2D but the plain black on the gamechanger is actually a pretty classy look on stage. If you like taking pics of your guitars by themselves then the Y2D is a winner. But I honestly think that too pretty of a guitar can distract from the player. Sounds silly, I know, but a painted simple finished guitar puts the focus on the performer, not the instrument. I want my playing, performance and tone to be the focus of my performance.
Plus, if you get a ding on a painted guitar it just looks better. Steve's #1 looks great to me. You gotta earn your relics! You get a ding on a Y2D and it looks terrible...and makes you feel terrible. (My Morse's are in great shape but I got a ding on my Petrucci that kills me every time I look at it).
Executive summary: Both great axes, no wrong answer.
The GC gets the nod as a gigger for flexibility and it's simple classic looks. It does almost everything a Morse will do and a whole bunch it won't and get's you closer to a "1 and done" solution.
If you want a beautiful axe for the studio and you want some name/brand recognition maybe lean towards the Y2D.