Fair enough - I'd just guess that PE kinda snowballed over time, and since it's the biggest name, of course it's become the default.
I think Unity's a good program to use, for two big reasons: Primarily, my goal is also something more akin to the 2.5D generations(Diamond/Pearl/HG/SS and Black/White/B2/W2). Secondarily, I'd like to see a bit more diversity in publishing - Unity's got build options for just about everything these days, and there are a lot of times that the test builds for fangames seem not to really warrant downloading a whole build. (And personally I like browser-based implementation a bit better :P )