I don't think it will matter at D2 or D3. It will matter at big schools. Like Syracuse going from the Big East to the ACC. But I hardly think a coach who's winning at Syracuse or Louisville or Notre Dame is going to be upset and quit the game if they move from one power league to another.
I think the game could use some updates so it doesn't feel so hopelessly out of date. I don't think ALL realignment has to be fixed. But some obvious and easy fixes could make the game at least a bit more realistic. Like move Hawaii and Fresno out of the Pac12 and into the MWC and Utah to the Pac12 and TCU to the Big12. Then move Colorado about out of the big12 in place of TCU and into the pac12. Those are all easy changes that will not upset many and will add some extra realism to the game.
It gets more complicated in the power 5 because the conferences are larger and the game (for whatever) reason has to have equal conference numbers even though I think it's more boring to have it uniform. To me it doesn't hurt the game to have one conference with 15 schools and one with 10 but I'm sure it's a hard thing to fix.