How long do Magic rounds take? How do their tiebreaker scenarios break down? How many of their games will go to time in any given tournament? How much extra time does their tiebreaker system add to the tournament?
All of these are questions that have to be answered. I'm pretty certain that I know the answer to some of them just off the top of my head.
Magic does allow Draws, which is something that I believe should NOT be incorporated into Pokemon at any level. They are bad for both competitive AND casual players alike. They're bad for competitive players because they allow players to directly manipulate the top cut with absolutely no drawback to the player. Currently, that can happen at only one table (the top table in each age group). If you allow Draws, you also allow for tables all the way down the line to manipulate the top cut. Not only that, but you'll get stalling and speeding issues far beyond what we've seen thus far. If players know that they can play for a tie, and they know that they're in a losing position, it becomes MUCH easier for them to slow play and still maintain points at pretty much any time during a match. They're bad for casual players, because they want to play the game as much as possible. Allowing draws means that you're allowing games to go incomplete, which is unsatisfying for the casual player.
Pokemon does not allow ties, this is something that we've agreed is a good thing much earlier in this thread. This year, we also introduced a tiebreaker system in BO3 scenarios that ensures that a second, meaningful game counts while also virtually ensuring longer round times. I like the BO3 tiebreakers, as they allow for up to three long, intense, meaningful games in an amount of time that it would normally take to play 2 games. Don't believe me? Game 1 lasts 40 minutes, a nice, long, involved game where there's back-and-forth and goes down to the last prize. Game 2 lasts 20 minutes, ending with the losing player taking his 4th prize as time expires. Then, you have a one prize sudden death game, which can last anywhere from 30 seconds to ten minutes (I've seen these before). It's a FAR more satisfying conclusion than having one player win game 1 and then slowplay game 2 for the win.
Now, if you agree with me that draws are not good for this game, and if you agree with me that the new tiebreaker scenario IS good for this game, then you've painted yourself into something of a corner when proposing BO3 Swiss rounds. Even if you reduce the round time to 45 minutes, it's all too common to get into the Sudden Death tiebreaker after game 2, which will last probably around 10 minutes, not to mention the standard turnaround time for getting into the next round or a game 2 tie that needs to be broken. By going to 45 minute BO3, you've essentially added 15-20 minutes PER ROUND onto the tournament time, making each round last 1:15-1:20. Now, for most Masters, this isn't necessarily a bad thing. Many Seniors wouldn't mind either. But the Juniors are the ones that I'm concerned about here. in general, their attention span is far less than the Seniors or Masters, and they wouldn't hold up over a long day. Also, most events (in my experience and IMO) are understaffed, even as the events get larger and more intense. So, you're essentially putting more strain on an already strained volunteer staff that's already working upwards of 18 hours in a day (and longer with BO3 Swiss) to implement a system designed to benefit the players that PCI does not market its game towards. PCI has always marketed its game towards the Juniors and, to a lesser extent, the Seniors. The Masters are included mostly to keep the Jrs and Srs happy that they can keep playing after they age up, as well as to give the JR/Sr parents a chance to bond with their kids.
As far as the comparisons between Pokemon and other TCGs, including MTG, there are always going to be obvious similarities between any TCG and MTG. WOTC pretty much perfected the TCG and CCG over a decade ago. At the very least, they popularized it with MTG. The reason that many games take ideas from MTG is because that game works, plain and simple. You can find elements of MTG in every single TCG that's been made since 1995, even if only in broad strokes. Pokemon is closer than most, but it's still distinct enough and has its own unique concepts (evolution, unshared resources, modular deck typing).
Everything that I've said above is strictly IMO.