invest points in hacking
That's not challenge, that's bad design. Nowhere does the game hint on you having to use hacking in the end.
While you could argue the very nature of the villain could imply the usefulness of investing hacking, fact is, you don't have
to use hacking. It just makes the fight far easier.
There is the replicator holding the Sympathetic Resonator, but an ICE pick takes care of that. While I agree that it creates a potentially unwinnable situation and is thus an example of bad design, I would imagine most resourceful players kept at least one at hand at all times for emergencies like that. Potentially easy solution would have been to stash a pick somewhere on the Command Deck.
As for difficulty... I unfortunately had to play SS2 on Normal mode as it was my first first-person game with a keyboard and mouse setup so I was expecting to be utterly useless, though it was much easier than anticipated. So I speak mainly in regard to console gaming or slow paced PC games, but typically I find games most enjoyable and satisfying when they are at their most difficult, providing that difficulty is well thought out.