The changes include:
1) All military transports should now be able to carry planetary assault forces.
2) Many heavier ship hulls have more system hardpoints.
3) Your science leader's abilities should now function as per their description in the Technology screen.
Also -- in the not too distant future, there should be a patch notes system in place, so you'll see notices of this sort when the updater is downloading new builds

Many thanks for all your helpful feedback!