O.k I have a couple of issues late game, i'm sure everyone who has played a moderate to large sized game that has progressed to the ending stages will be aware of these.

 Unending games - yup, once you reach a certain stage the game cannot be ended the majority of the time, TEC gets their powerhouse economy up and running and can spam ships faster than you can kill them and the vasari opens up RA and starts spamming more ships than you can kill but it doesn't cost them anything.

Oh yeah and advent realises they shouldn't play big maps =/

 Capital ships - capital ships late game become worthless, in fact they often do before that. Why should my two lvl10 capital ships that it took 4 hours to lvl up have to run away within 45 seconds of every battle? They're worthless after a certain point and they don't even take enough damage to make a difference in the overall battle.