Probably the most important difference right now is the size. The simple fact that Hubski is smaller is conductive to a very different community and type of content.
Of course that will change with time, but aside from that the site mechanics, while initially seeming very similar, make a big difference.
The two largest most profound differences are that 1) there is no downvote button and 2) you follow people.
The absence of downvoting or equivalent cannot be overstated. It changes the discussion in that there actually is some. You can't just dismiss opposing views and suppress them. People post what they think without fear of retaliation or hive-minding.
And the fact that you follow people instills an innate sense of community. I will never feel a sense of community on reddit, nor likely even recognize any users there from one post to another. Yet on Hubski I sense that I know something about the people I interact with. I even communicate with them outside of the website.
The other issue is that Reddit is absolutely bloated mechanically speaking: the site mechanics are terrible for what the site is now. They've been piling-on band-aids for a while now: subreddits that tag posts, add flair, disable downvotes, multireddits, mods clamping down on rules, the fact that half the site uses RES, subreddits undergoing mitosis to divide shit and quality content, endless subreddits centered around promoting discourse "the way it should be", etc.
Reddit right now is layer upon layer of tacked-on mechanics that are trying to fix the fundamental flaws of the site which stem from its huge population, voting system, and feed ranking system that discourages deep, time-consuming content. Right now browsing subreddits is like jumping from one ugly geocities site to another.