My idea is that the Ancient Ruins special, which currently (in my version) gives a free tech or building to the empire, could also perhaps give a free ship, or fleet of ships, with very special hulls and parts which can't be unlocked and built normally.
Has it been considered that instead of changing the one ancient ruins special that we already have, we could perhaps add more specials that deal with lost civilizations and stuff that they left behind?
Here are a couple of my very early ideas on this topic:
We could have for example ancient ruins of an advanced civilization special, which would give you a research bonus like the ancient ruins special currently does.
Then we could have an ancient ruins special of a civilization that never achieved an advanced (space travel) stage and so doesn`t offer very much in terms of technology. This special however might give you a bonus in trade, as it could attract tourists from around the galaxy to explore galactic history and to reflect their own values to the ruins. And even if your particular culture would see the ruins only as meaningless traces of the past, the ruins could still probably be turned to profit, by selling the found unique artefacts/buildings to those who consider them valuable. (I am currently not sure, if the ancient ruins special of an advanced civilization should also receive a trade bonus. It could probably however make sense either way, as one the one hand ruins that are capable of offering you a significant research bonus would probably be off-limits for most of your citizens to avoid revealing any usefull information to enemy spies, but on the other hand if visitors are allowed to see the advanced ruins, they could possibly gather more people than less advanced ruins.)
In addition to these, we might have the kinds of things that you suggested like hidden/crashed ships or fleets and technology that the ancient races left behind on various planets or solar systems, as independent specials. (Although perhaps in some cases also combined with the ancient ruins specials.)
If I can remember right, something a little like this was once already suggested by marhawkman, but in his suggestion there were also ruins that didn`t have much positive to offer, which is something that I myself oppose, as I would like to see each trace of a lost civilization to offer something usefull to the game.