Let me add a few more house rules then:
1) upgrading ships is fine, but you may not upgrade into a different ship type. Ie no colony ships to transports, constructors to colonies, sensor boats to trade, etc. Upgrading to differrent weapon load outs is fine - ie beam to missile.
2) maintaining 2 opposing ideologies at once should probably be disallowed. ie having a death furnace running while bee lining down benevolent ideology tree makes no sense.
want to beeline down benevolent? Destroy the furnaces etc.
optimally this would not be disallowed, but just discouraged through stronger penalties.
the idea being that it makes total sense to have a benevolent republic slowly morph into a genocidal xenophobic empire - but usually such changes are somewhat gradual or if done quickly they are accompanied by drastic social upheaval.
in civ5, your empire must be unhappy before you can change "ideologies".