Well, three things:
1. It needs a persistent connection. Now, I know it's just a little data here and there and whatever, but as someone who travels a lot in area where "internet connection" sometime means spotty 3G and walled garden wifi, it's a huge issue.
2. We're by design never going to get mods and player made missions/campaign and other goodies.
3. Overall even without clear things to point out, I can't help but feel like the game has been designed with that multiplayer system in sight and had to mold its balance / economy / gameplay around it, so a solo experience could be different (and possibly less "do your own experience with the other players, because the game doesn't have that much").
Still enjoy the game tremendously, but to be fair what I wanted was Elite 3 remastered more than multiplayer Elite.