I see two issues remaining:

1) # of cities vs prestige - kills city growth after 10 or so cities.  If they are insistent on this restriction I think the increase to building prestige noted by others is the best solution.

2) Combat - in tactical combat hand-to-hand damage is dealt simultaneously even if the first attack kills the opponent.  The attacking unit however is still on screen with 0 health in some cases and only dies after combat ends.  You can heal the unit up once so they survive otherwise they just disappear.  This doesn't happen if you auto-resolve combat.

Please fix these two issues in 1.4 so at least you can play this game if you wish to.  It is fun but these just make it an hour of irritation.  Also the AI doesn't ever seem to be able to cope with the new rules either for city management-research and growth so it would help across the board to alter the city # limit.