I too have both. I learned pen turning with bowl tools and as a result like the longer shafts. However, in two weeks I have adapted to the shorter Pen Pro just fine and like it. I also ordered the Uni-tool and like the longer feel.
In reality, it is what you are used to and feel comfortable with - more so than the fact of one being longer or shorter than the other.
A warning of sorts is that the different inserts that come with the Uni-tool each have their own "feel". To me, the 4" radius has a different feel from the straight, and the 2"R and round have a different feel also. In some ways, the straight and 4R are similar but the edge of the straight will grab more than the 4R if rough turning down a blank to size. The 2R and round also have a different feel and require a good knowledge of them before jumping into an expensive blank.
I find a bit more distinction of feel in the inserts - than the length of the handle. Having said that, I prefer to use a longer handle for the 2"R and round because of the stronger grip I get with the longer shaft. What I am saying is that the 2R and round will have a tendency to grab more in some situations than the 4R. These are my experiences and others may be different.