Mainly the transitions and lens flare. Remember that Universe is very new so there will be additional offerings over time. I have used Red Link in the past for other Red Giant products and it has made updating very easy not to mention other products that might be of interest. In my very honest opinion, without question Red Giant really knows how to innovate and keep their customer base very happy in the process.
Some native plug-ins (ones that come standard with the application)usually do a very nice job. Sometimes it is a tie and sometimes there is a clear winner. I think that Red Giant does offer very good quality products. I have purchased Trapcode Particular and have been very satisfied with that purchase. So far the same goes for Universe and the amount of free stuff really made the decision to subscribe that much easier.
Will the competition take notice and offer something similar? My two cents, whatever it is worth.