I don't see why they couldn't potentially be fun with an expansion specifically designed to make them playable. There are fun ways to approach playing as a crumbled state. For example, there could be mechanics that have you work towards unlocking one of the normal features of empires on success. In doing so, you may provoke a civil war, suffer pop unhappiness, see some of your starting ships desert, etc. The most sensible final reform would probably be to declare war when you please, enabling you to win a conquest victory.
Interacting with other empires could trigger various effects depending on what you do and your ethics. If you're a fanatical xenophobe and want to fight the end game Cthulhu monsters and they're on the other side of the galaxy, you may have to sacrifice one your hard fought reforms or risk a coup that orders the fleet home.
The hardest part would be Day 1. EUIV's fallen empire has normal diplomatic options and gameplay mechanics while you work on restoring its ancient glory. But some kind of story driven start could overcome that. Perhaps you don't begin as the leader of the FE, but as the equivalent of a sector governor and must first struggle to retake the reins of history.