They also take away the flashing "counter" indicator which does make it quite a bit more difficult.
Actually, I believe the counter indicators are still present in hard mode; they're removed for New Game Plus (which is easier, in my opinion, as you start off with all of your gadgets/abilities).
I've played through Arkham Asylum and Arkham City a few times with a mouse and keyboard and I've found them both to be quite easy yet incredibly satisfying. The key is to know the mechanics of the combat system. I recommend reading the "Combat Mechanics" guides by abaddononion2 on GameFaqs:
Arkham Asylum:
http://www.gamefaqs.com/pc/952339-batman-arkham-asylum/faqs/57661
Arkham City:
http://www.gamefaqs.com/pc/982135-batman-arkham-city/faqs/63221
It's also very helpful to watch good players complete some of the Challenge maps on YouTube so that you can emulate them in your own battles:
Arkham Asylum:
http://www.youtube.com/watch?v=7_l0T6i5Pm4
Arkham City:
http://www.youtube.com/watch?v=AEVSjqGfBFQ
Keep Batman flowing from enemy to enemy using evades or Freeflow/Critical strikes. Target enemies by looking at them with the mouse even as Batman is completing his previous move. Use gadgets for crowd-control. When in doubt, evade over an enemy (although beware of accidentally initiating an aerial attack). Merely avoiding button-mashing to chain together critical strikes isn't quite good enough; you want to adopt the correct rhythm for your attacks. Initiate the next strike too quickly, and you'll jump straight into an enemy's attack. Attack too slowly, and you'll be struck from behind (and/or you'll lose your combination). Once you get the timing down and are aware of all the appropriate counter-moves for the various enemy attacks, you won't get hit unless you screw up. The titans do make things a bit harder; you'll have to be aware of their locations and evade at the right time.
After you've internalized how the enemies attack, how Batman moves, how combinations are started and retained, how to use your gadgets as part of your combination, etc., the fighting becomes trivial. Fighting 10 enemies becomes the same as fighting 100 enemies. In fact, you'll
want the thugs to be tougher/more numerous because then you can beat more points out of them.
That's right: when you have mastered the combat system - when you have truly
become Batman - you will realize that the enemies are not actually hardened, muscle-bound criminals that threaten to bash your head in with crowbars or riddle you with holes from an assault rifle. They're not even warm-ups or speed bumps on your way to saving Arkham City from Gotham's most powerful supervillains. They are, in fact, point dispensers. You hit them, and points come out. And the more points Batman gets, the happier Batman becomes.
Arkham City may be a hellhole for most, but for Bruce Wayne, it's heaven. It's his own goddamned private playground, built and paid for by the citizens of Gotham. Let him live his dream by beating the crap out of lowlife thugs as often as you can.