1) While it does nothing to encourage people not to play (like Elo), it does not provide incentive to play events after reaching a certain threshold
To the best of my understanding, the PWP system was created in order to provide incentive for the best players to play in an increased number of events. By no longer providing incentive to continue playing in events (of course I could be wrong here if there's some sweet rewards for the new "Pro Players Club" that have yet to be announced, but we can't speculate on that yet) it takes away the fundamental reason for the system. Why would players show up to GPs/PTQs/FNMs if they feel safe in having reached the threshold to qualify for the next PT already.
2) It provides a gigantic advantage to people who are qualified for the current season's Pro Tour
Pro Tours are now 16 rounds with no cut to day 2; 16 guaranteed rounds at an event with a 12x multiplier is HUGE. Let's take someone thoroughly mediocre who goes 8-8 at a PT: that's (8*3+6)*12=360 points. To get the equivalent number of points in a GP (which is an 8x multiplier, but has more participation points), you'd need (3*x+7.5)*8=360 gives an x of 12.5. So in order to catch up to someone going 8-8 in a PT, one would need to T8 a GP.
3) If the Y is small the same pros would always win the tickets, if Y is large the system is no different than the current one
Well the case of small Y would be what I would prefer to happen (which would hurt me), Wizards has made it clear that this is not what they want. They want a system in which everyone (no matter how false this impression is) to feel like they can q for the Pro Tour just by showing up to every local tournament possible. They want a system that encourages people to keep playing in more events, not one that encourages people to show up to a few GPs, a PT, and not anything else.
4) It completely eliminates FNM from the PWP picture
Unless Wizards does something like A FNMs, B PTQs, C GPTs, D GPs, and 1 PT to make the Y events, there would no longer be a reason for anyone hoping to q off PWPs to show up to FNM. As getting better people to go to FNM increases interest in competitive play (I convinced a few people at my local store to go to some PTQs and I'm just some mid level grinder. I imagine Kibler/LSV/others showing up to your FNM would be pretty cool, even for those who don't follow the Pro Tour). I assume the reason that Wizards placed FNM on such an important pedestal (I mean, it's not like playing Magic on Friday night is much different than any other night. Unless wotc is just trying to get people to give up their social life in order to play....) is because they want people that wouldn't ordinarily show up to show up.
5) It makes the regional imbalance even more absurd than it already is
The next season has 15 Grand Prixs, 9 of them are in North America, 3 in Europe, 1 in Japan, 1 in Australia, and 1 in East Asia. If the top X event system is implemented, I see absolutely no way (the regional slots would go to the few European pros who travel frequently) for any non-professional outside the US to have any chance of making it. Going 6-3 (a terrible record) at a GP is worth more than losing in the finals of an 8 round PTQ, basically giving no chance of qualifying to the non-American grinder.
6) PTQ grinders who don't travel to GPs have no chance
One of the aspects of the PWP system that was almost universally lauded was the fact that it would reward players who consistently perform well at PTQs. Under the new system (unless, as previously mentioned, Y is large which would essentially really be the same system as it is now) the player who T8s multiple PTQs would do significantly worse than a player who shows up to GPs and fails to day 2; the system would reward the ability and willingness to travel over consistency at the PTQ level which I don't think is their goal.
Please feel free to discuss and critique my points either in the comments here or on Twitter.
@dieplstks on twitter