My own desires (which are probably not in line with everyone else, but hey, you asked!):
First, I'm REALLY wanting the Alpha empires rounded out. So the ISC I think are the only empire really missing, but Andromedan ships would be completely wonderful as well. That more-or-less gives me that full "core" set of empires I want to play with.
Once they're added, I'd love to get expanded support for either more "minor" or extinct empires (Vudar, Jindarians, Carnivons, Paravions etc) or an "early years" set of ships and rules (like FC Briefing #2), or support ships (like in Briefing #1) or maybe at some future point X Ships. And there's Omega to look at at some point, plus the LMC if that's not enough.
I know this probably isn't the most popular opinion, but I really just like the SFU as large ships fighting each other. Once you have all empires having fighters and then interceptors and PFs, to me you're playing a very different game and not one I'm really all that interested in. The Hydrans having fighters is cool and all, it's their "thing". There are other popular Sci Fi setting which concentrate on smaller ships and fighter combat and to be honest I'm more interested in using those settings for that type of thing. So what I want from the Starfleet Armada line is more "proper" ships of all empires and types.
I think the only FC products not yet converted are War and Peace, Transports Attacked and Battleships Attack, plus the Briefings, so getting those converted makes complete sense (I'm assuming that this is what you're doing anyway, since that's what you've done so far!).
If you're asking about other content, I'd really like to see some more scenarios. Whether these are conversions of old FC/SFB scenarios from various sources or new, I really don't care. But it'd be cool to have even some vague and fairly generic scenarios worked out: generic escort, base defence, asymmetric forces with different objectives, that kind of thing.
EDITED TO ADD: Oh yeah, and MORE SPACE MONSTERS PLEASE!!!