@Bryan: I haven't played in any of the championship events before because I don't have the money to do so, nor am I likely to play any in the near future. For that reason, I can't really comment on them specifically. My experience comes solely from playing micro-stakes MTTs on a recreational basis, but have been doing so since 2007 so I've seen quite a few different structures over the years. My answers below are based on that experience.
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When it comes to someone coming into an Event with a starting stack, while the average stack is perhaps two or three times the starting stack, how does someone coming in at a relative disadvantage affect the dynamics of your table (and/or the overall Event) more than someone whose stack has dwindled down to that same level being moved to your table?
My concern here isn't so much related to the size the stacks when compared to other chip stacks, but rather in terms of big blinds. As late-registration nears the end of the 2 hours a starting stack is only about 10 big blinds. If a player has built up a stack of let's say 100bb, he is unable to use it to see flops and make decisions on later streets when 3 or 4 players on the table have just joined with short stacks. If late registration was not in play there is usually only 1, or maybe 2, players who's stacks have dwindled so short, which isn't nearly as bad.
The only way to solve this (IMO) is to update the structure so that the starting stack is deeper at the end of late-registration. To accomplish that we need either a slower structure, deeper starting stack, or shorter late-registration. The first two will make the tournaments even longer, which is not desired.
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...is the ability for late registering players to significantly amp up the prize pool worth any potential annoyance to you?
With the awareness that the regular tournaments are handled by Luke rather than yourself, I would ask if the number of players that register in the second hour of late registration is "significantly" more than the number of players that register in the first hour (assuming only two hours of late-reg). It also depends on what you feel is a "significant" boost to the prize pool. If I have to play for longer to earn the same minimal prize, then no, the bottom prizes simply aren't worth it (or even the middle prizes). If it means earning 50% more when making a deep run but only requiring an extra hour of play then sure, but the deep run is a rarity. I play micro-stakes tournaments, so the money is not significant to begin with, and on the recreational side, my time is more important to me. I play to enjoy poker. When the pre-bubble portion feels like it is dragging on and on, I start to lose my enjoyment.
26sk8er make a good point as well, and is actually something I have commented on (to myself, while playing). When I am 90 minutes into a tournament I want to be able to look at the number of players remaining and see that number lower than it was 60 minutes into the tournament, and not by just one or two players. Because the number hardly changes over the last 25% or 50% of the late registration period it feels as if the tournament is not making any progress.
BTW, thanks Bryan for popping in to comment on the thread