Late to the discussion, sorry — but I entirely agree.
There's already a very, very basic mod out there that allows for multiplayer, though it's more a proof of concept than anything actually fun. I say this as a massive fan of the game, and someone who thinks playing it solo is THE best way to experience the game, but multiplayer would be pretty fun and a good way to add replayability.
I think I'd love to see the second player either take the role of Ena or, hell, given it wouldn't strictly be the canon mode, even an Ariral character or just a player-controlled Omega Kerfus would be really fun to see.
I know it'd be really hard to implement, both because of networking and also because of how a lot of the events are scripted, so I'm not holding my breath for it—besides, Dr Nose has final say on whether or not he even wants multiplayer as part of the base game—but I don't think it'd ruin the experience.