First of all, while I was hoping for more dogfight style space combat, Star Fox 2012 is fine by me, so I'm fine with the rail shooter/ship upgrade system; since that's what it is, no major revamp needed.
Now, some suggestions:
1. Change some of the mission and bonus mission text to more accurately reflect what is being requested. For example, "Decimate" means 1/10. Not 14/50, or any other derivative that is not 10%. "Obliterate" doesn't mean "kill about 60% of" it means "leave less than 1% alive to spread horror stories." "Destroy" is generally well used, and perhaps needs to be used more. "Cripple" is also a nice, well-used one. The addition of "hinder," "impair," "reduce," "mitigate," and other thesaurus selections might add some variety, while also providing accuracy.
2. When on the selection screen, let me know the time of the impending space combat so I can accurately select the right mission for my ramen cooking needs. The limited time factor is a great thing for a minigame of this sort--it would be nice to not have to reference an external list to figure out how much of a timeburn I should anticipate.
3. Give me an option to shut my companion up. It would be better if she would react more correctly to the events (not "you did learn how to fly, didn't you" when I'm at 100% shields and hull and have accomplished all of the bonus objectives), but probably easier just to code a mute button for them--without making me miss out on the explosion goodness. In fact, let me mute my companions unless I'm specifically talking to them, or have summoned them. But that's slightly off topic.
4. Correctly identify "frigate" and "capital ship" in mission text. For example, when I have to destroy 14 capital ship turrents, and the bonus mission is to destroy 75 enemy fighers and capital ship turrets, but the latter ACTUALLY means "frigate turrets", it is a tad confusing, and immersion breaking.
5. Is it really necessary to have "missiles useful" beside every main mission objective? When I'm squashing 60 talon fighters, are missiles any more useful than they would have been on the bonus mission to squash 75 talon fighters on the last mission? A bit less text clutter would be nice, overall.
6. This is the game of the voiceover. Why isn't there a fleet admiral setting up each new mission as I get it? (Not for the dailies, but with the introduction of a new space mission, it would add something to what otherwise feels like a cobbled-on add-on.)
7. More things on which to spend my fleet tokens. Consumables for ships? An astromech that can go repair my hull? A dancing girl for my bridge? Matching flightsuits for my entire crew? Purchaseable space missions? The possibilities are endless!