The biggest difference is the lack of a single-topic community like reddit.
Reddit has subreddits. Everyone submits content to the subreddit. What ends up happening is every subreddit is a bubble based around a community sharing essentially the same things. The results can be great (like TheoryofReddit or the niche topic subreddits) or horrendous (like atheism and politics.)
The way the reddit system is designed, its easy to fall into a huge circlejerk because you are only seeing posts from like minded people on a single topic. If people have the same interests, thoughts, opinions as you, how are much room is there for expansive learning or growing? You see this is both the posts and the comments across reddit.
Hubski on the other hand is based around following people. People that may have the same interests as you but also have interests or opinions that you normally wouldn't subject yourself to.
I may be following someone that posts and shares great music, but I also see their posts about dumpster diving. This mimics real-life relationship more and gives more diversity and serendipity. No one has the exact same set of interests as other people, but hanging out in /r/atheism for too long and you will no longer be challenged by new ideas, opinions, or topics.
The other difference with following people, is you start to notice usernames much more and the community and relationships you have with other users here grows over time. It has to do with the quantity of users as well, but I consistently recognize usernames and associate the name with past discussions I've had. I have gotten to the point where I usually know who the poster is before even looking at their username. It's a small detail but it makes the community stronger, IMO.
You don't have to chose one. I consistently visit reddit for the graphic design / freelancer / startup subreddits to get my fix of inspiration and critiques. But when I'm looking for a high-level discussion or some mind-penetrating articles, I am here. It is harder to find those long discussions or deeper level thinking on reddit these days.