I'd like to propose for Transcendence, at the start screen, a box opposite the score box that has a tip, hint, or bit of backstory on it, which changes each time you revisit that screen (by dying or quitting hte game and re-opening).
I think it's a good way to slowly introduce new players to complex features without shoving it down their throats via a manual (I love a good manual though ), and it's easily ignored by veteran players (unlike the current flashing messages, although I'm not proposing this as a replacement, it could be)).
Some possible 'tips' (add your own):
Little tidbits of backstory: talk about the Iocrym and the quarantine, Domina, the Ares War, etc. Currently it's impossbile to learn much of this ingame.
One for each faction, describing their ships and whether they are hostile or not.
Messages hinting about notable items/places (mostly useful if Transcendence becomes a little less linear and there is more secret stuff), like "St. Katharines is the center of Commonwealth blah blah (see? I don't even know what it's the center of!)" or "the Qianlong Archcannon is perhaps the most feared weapon in known space. Something about antimatter hinting that Longzhu Spheres would recharge it goes in this sentence"
Less obvious gameplay hints like:
"Most commonwealth stations will decontaminate your ship if it becomes irradiated. For a small fee, of course."
Depending on whether the messages are "in character", there could also be semi-fluff advertisments for corporations (although they serve the useful purpose of telling the player about cool stuff):
"When 'incendiary' just isn't enough, try the Gotha missile line. Nothing stands in it's way. Rasiermesser: Insert Corporate Slogan Here. "
etc, etc, not to mention Anarchist propaganda if you in-characterize this as a news ticker.