The only real changes DX:HR needs for hacking is
1) Fewer instances of it to make it less repetitive. Multitools or simplified minigame for keypads would be fine.
2) More varied rewards (emails!) for poking around systems
The system itself is fine, but you do it too often.
Heck if the hacking is more seldom and the # of viruses you accumulate is scaled down you could handwave that automatic antivirus updates get distributed which renders your virus unusable; every virus you get is unique and that is why they are a limited resource.
I'd change the system a bit:
First, I would connect all terminals in at least part of the building in a single subnet rather than having separate network for every terminal, so with good skills you'd be able to crawl around the building accessing data and various systems without physically moving from your original access spot.
Second, I would vary, or rather remove defined goals - instead of having registry nodes that would make the network 'hacked', there would be simply other terminals with data on them, dedicated datastores (data not located on physically accessible terminal) and API nodes corresponding to physical stuff like power sub-grids or individual door keypads - so you could open the locks, deactivate lasers, or switch off power to stuff like lights, elevators, some parts of the network (like security server if you knew which part of the grid supplied it, or some routers to temporarily cut the trace off).
Third, I would make skill/aug level affect hackability of individual nodes (and maybe probability of detection during hack).
Fourth, I would make you able to bypass hacking of entry point if know the password. Moreover, the more privileged the account you'd be using the more stuff you could do the easy way in the network, being able to do a lot with subordinate systems without alerting the automated security (wetware guards would obviously get suspicious if you started fiddling with environmental stuff regardless of your privileges) and only having to hack it hard way upwards. Hunting passwords would suddenly become very important even for the 31337 d00d.
Fifth, I would vary the security measures.
Sixth, I would move from resource based mechanics to a tool based one, including stuff like employing decoys or putting a backdoor on a different terminal you don't know password for, disconnecting to evade trace, then physically moving to the machine with backdoor to start again from a non-compromised access point.
Still, overall it would be a very similar "click the nodes" minigame, and even the original is simply the best hacking minigame in similar game, if only because it actually tries to depict network as network rather than "connect 3" (SS2) or pipe-game.
DX1 progress bar also wasn't very inspired and got in the way of reading.
Wouldn't be that hard to make the DX:HR sequel better though.
1) Limit Praxis points (so you can't do everything by the end)
I'd rather just tweak the cost of different abilities based on power.
Abilities with very short trees (like typhoon) can be very powerful, but cost very little in current skill mechanics.
This would eat excess praxis points as a side effect as most abilities cost 1, tree-rots 2 in current system.
2) Fix boss fights (alternate ways to handle)
Yeah, even a hackable turret/bot, some architecture usable by mobility-augmented individuals or breakable walls would really help those fights even in their current shitty form.
4) Better pacing, don't rush the end.
I'd settle for "don't derp the end".
5) Make take downs less derp, simple throat slash, neck break, asphyxiation please.
I'd settle for real time takedowns and typhoon, as well as noisier non-lethal beatings to make player actually think before using those abilities (because he would be gunned down if there were multiple enemies around in a position to shoot him).
Would reduce takedown energy cost in exchange, because in a perfect world punching someone in the face should not take a full candy bar.