From what I've played, the new Armageddon rules are a great improvement over the old tourney. But of course it's whatever you're comfortable running, you need to be familiar with the rules yourselves to settle any possible rules disputes!
If you go with the old tourney rules, can I recommend the usual modifications: Shadow Hunter is hull 5 not 6 but gets free fighters, and Sagittarius is Raid level.
I'd also recommend modifying the hyperspace rules, since the old tourney pack pretty much arbitrarily gives one player an advantage. Either both players can keep up to 2 FAP's in hyperspace, or nobody gets any hyperspace. Both those options are much fairer IMO than rolling a D6 for who gets a hyperspace advantage.