Played for about a dozen hours on hardmode already (don't ask!).
Here's what I've encountered so far:
[ul][li]Hardmode kicks my ass - I can't say how much but I definitely needed a lot of restarts with what I tried instead of a few that usually led me to victory in normal. I also have the distinct feeling that repair speed for enemy ships has been increased a lot while your own has been diminished, which is very very annoying.[/li][/ul]
[ul][li]Boarding has been nerfed: teleporter is more expensive, successful boarding yields less scrap and the Flagship is less susceptible to it. The middle point might be due to hardmode, though.[/li][/ul]
[ul][li]Autopilot is more useful: Now provides a far higher (50/80) bonus as before and can actually be useful in the game.[/li][/ul]
[ul][li]Door System can now be manned: Manning it gives instant access to the next higher tier which is extremely useful to reign in fires or boarding parties.[/li][/ul]
[ul][li]More stuff that breaks shields: hacking provides a nice way of draining the shields without having to resort to endless Laser-salvos or missiles to get through. The new flak cannon and vulcans also do that job pretty decently. [/li][/ul]
[ul][li]Mind Control & Cloning Bay: Two things I haven't tried yet but endless boarding parties due to cloning are a nuisance - the mind control much less so, because it usually wears off quickly enough so that occupying the controlled person with another of your crew members and bailing out when it becomes dangerous for either suffices for the effect to wear off before any systems get destroyed.[/li][/ul]
[ul][li]Hacking: probably the most useful new system in the advanced edition for me so far - provides lots of options, some of them really devastating (shield and weapon drain!) and doesn't cost too much. Sweet![/li][/ul]
[ul][li]Harder Boss: yes if you thought that thing was already hard, think again: level one now also hacks you and the layout has been changed slightly so that the crew has access and can repair the missile and laser system. Annoying. Got quickly shot down at level two so can't comment on the other levels yet.[/li][/ul]
[ul][li]As said, access to ships is far easier and C types seem to unlock upon reaching sector 8 with the B type already.[/li][/ul]