In a way, absolutely. Having it as-it-is cheapens the effectiveness of everything you invest in doing role playing your game. Going forward, they're going to increase how much your in-game character is involved in the changing tides of the simulation. This only further makes jumping modes to circumvent things going on in Open more damaging to gameplay. Why would anyone even bother?
Note, I'm not talking about players moving around modes and doing their own thing. I'm talking about players who are moving around modes to accomplish activities with the purpose of affecting the background simulation either via community goals or by coordination via the faction influence method.
Promising single player was stupid, offline even more so. Creating a massive galaxy where you have no hope of ever becoming singularly significant and then playing it alone is not in any way interesting. It sounds like those players who wanted that wanted to play basically X3:Elite. Promising that the universe is shared between modes and then allowing players to freely switch between modes is more so stupid. It's obvious that FD hoped or maybe still hopes that there is no advantage in gameplay to switching between modes and so the shared universe will make sense but that's not the case. For the game to be interesting in the long run, that has to be addressed.
2 simple ways to do that would be to split characters such that your open character is separate from non-open. This has the added benefit of not needing to have separate background simulations. However, I'd still want to see different community goal rewards in place for open vs non-open mode, and the rewards would be locked to that mode.
The other way is different simulations per mode. This is the cleanest because it does away with the facade of a player having a legitimate use for jumping between modes other than to make certain activities easier.
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Also - No No No
The three modes all affecting the same Galaxy(Universe) is perhaps the only way to prevent the game being taken over by -
Heavyweight Gamers (good-on-'em), Heavyweight Psycho Cheater Exploiter Gamers (BOO-HISS!!!), Cheaters, Exploiters, Gankers and Griefers.
The cheaters are using the shared galaxy aspect for that very purpose. Or do you not think almost all the massive amounts of cheating isn't going on in solo/group mode ? The very few that stupidly do it in open are the only ones you hear about due to no witnesses available in the other modes. If they didn't affect eachother, there would be no incentive to cheat your way in solo and then be ridiculous in open.