I personally feel that Raieggs is still a great choice for Nationals. Consider the current format for just a second. The most broken trainer/Pokemon combo at the moment is still the Holon Engine with Holon Castform's Delta Draw. Though there are some decks out there that try to fight against the combo (Mario comes to mind), that doesn't stop Raieggs from abusing Scramble Energy for a quick win... or at least a quick comeback. In addition, it's already been mentioned on this thread that all of the decks in the top 5 fall prey to Cessation Crystal, a tool that Raieggs uses best.
Though Infernape is still a tough matchup, being able to lay down an early Cessation Crystal slows Infernape down, and nearly any tool that's been used in Raieggs before greatly helps out in the Infernape matchup (Solid Rage gives Raichu a OHKO against Infernape, Energy Root prevents a OHKO from an Infernape with a Double Rainbow Energy, Strength Charm can be used here, Cessation Crystal has been mentioned). From my own perspective, the Raieggs vs. Infernape matchup comes down to three different things. One, early game setup -- if Raieggs is able to get a jump on Infernape by knocking out a Skitty T2, I can see the game quickly going to the Raieggs player. Two, being able to maintain control of the field -- in this matchup it looks like whichever deck is able to respond best to what the opponent does will win ("respond" here refers to being able to consistantly send up a Pokemon turn after turn to do something; since Infernape only plays essentially a 4-2-3-1 line, I see Infernape quickly running our of resources). Three, skill -- contrary to what a lot of people say, Raieggs takes a great deal of skill to be used effectively; the deck in the right player's hands can be destructive (didn't Yamato recently win a big championship with Raieggs?).
The other thing I'd like to point out is the fact that Flariados isn't too much of a bad play either. At a big tournament like Nationals, many people will overlook simple tech cards such as Switch or Warp Point in favor of something they see as more beneficial for specific matchups (how much have we heard about Mew* lately?). I can definitely understand the Infernape matchup being difficult, but unless the Infernape player plays Switchs or Warp Points in their deck (and who would with the retreat cost being 0 for 75% of the deck?), Spider Trapping a Delcatty automatically causes the opponent to burn an energy to retreat, which buys the Flariados player an extra turn. Using this early game can help the Flariados player setup responses to Flare Blitz on the bench. And if all else fails, just hope that they stay asleep (flips are a part of the Flariados matchup). Many people still consider Flariados to be a good matchup against MetaNite as well, and the deck destroys Shiftry. I'm not too sure about the Absolutions matchup, but there are a lot of ex Pokemon in that deck for Flariados to take prizes from (not to mention the fact that Flariados matches Absolution's speed).
To me, the reason that people might not want to play the aforementioned decks is because they're old. Infernape is a new deck, R-Gon and Absolutions are both still pretty fresh, and there is a ton of talk about the Diamond and Pearl cards and whatnot. I know that this seems like a pretty lame reason for why people wouldn't play Raieggs or Flariados, but after awhile people get tired of seeing the same thing used at tournaments. I know that I haven't seen MetaNite used at all here in NC recently, and it's primarily because everyone's hyped up about Diamond and Pearl combos. Sometimes, however, the best deck to play isn't the newest (consider the Silvestro's use of Polistall at the Regionals held in Florida). Sometimes the best choice for a tournament is something that hasn't been seen for awhile.
