If we'd like to keep doing a seasonal style, as opposed to tournaments, I would suggest scheduling a best 2 out of 3 match either bi-weekly or monthly, depending on where everyone sits.
It's far easier to set a time well in advance, so that everyone can clear their schedule, as opposed to dynamically filling matches midweek while everyone juggles IRL stuff.
This should strike a balance between making it easier to field whole teams without subs, while still ensuring that the same general format stands.
Personally, I'm of the opinion that a one-game format is less optimal, as the matches won't feel nearly as conclusive.
Anything can happen in a single game, you can have one team outplayed by another for nearly the entire match and then rally for a wild comeback, or you can have tight finishes. If there's only one game per match and you get one such scenario, this can leave teams feeling like their placement on the ladder isn't nearly as justified.
(ex: "Yeah, we lost that game, but we took down all their inhibs and they barely scraped out the win. The other match was a total stomp, and yet the scoreboard considers our losses equal!") With the 2/3 format, when the other team beats you twice it's awfully hard to argue that they didn't earn it.
I would like to say I've had boatloads of fun so far despite the hiccups, and I'm really digging FNL. =)