Personally, I think the game shape training and blank lineup issues have ruined the idea behind utopia slightly.
I don't. I'm not saying either of those things are good for the game, and it'd probably be a net improvement if both disappeared, but I don't think the effect is going to have any significance at this point in Utopia's lifespan.
Where it would be a much bigger concern is once we get to having serious talent in the top leagues, and the differences between teams is such that the relatively small effects of those issues will be heavier in comparison to the delta between the teams. But currently, there's much more variation of rosters and skill levels of managers. Accordingly, factors like GS training or blank lineups or noobfarming their bank accounts or lucky/unlucky starting rosters or the like pale in comparison to managerial competence in building and managing their roster and lineups.
The long and short of it is that Utopia is just another reflection of the user. A user that knows how to build a team from the ground up will be able to do that again. A user who knows how to profit by transfer list shenanigans will be able to do that again. A user who knows how to buy higher salary players, expect higher ratings, and complains when he gets beat by better-built teams will be able to do that again. Utopia is whatever we make of it.