They're filler yes, but I'm not sure they're just pointless, especially in Eva's case.
I mean, only appearance she had was with MC, Lilly and the rest of the navy's exploration group in the very beginning, then gets kidnapped and afterwards we don't see her until MC's group arrives at the Acarhyn planet.
Quite a long gap between beginning till that time with no Eva content so for Eva at least, the whole "Simul-Eva" storyline did make sense since MC missed his sister so much.
Makes less sense for Simul-Lilly case especially considering she started going psychotic
, but Simul-Eva was basically alone in the simulation and MC basically had to have someone to keep her company while he's not there.
Though I guess with MC's reunion with Eva (and her return to the Iron Bastard set to happen in the future), the big question is how Perv is gonna close up Simul-Eva and Simul-Lilly storylines (here's hoping they get tied off nicely, and not just tossed aside).