To some extent it's because shoujo is at it's heart of hearts about people and relationships, whereas shounen at it's heart of hearts is about things and stuff happening. Shounen isekai tend to get overexcited about their world-building (even though it's not terribly good, usually) and "power levels" and whatnot, which unfortunately the isekai genre lends itself to easily. On the other hand, human relationships work pretty much the same in another world so there's less room to get sidetracked into bad writing, in shoujo.
Complementing that, the "average" women's indulgent fantasies about romance (involving ever-deeper bonds with men of intriguing and/or flawless character and, of course, good looks) nonetheless make much better reading than the "average" men's (which are basically just foreplay and sex—I mean I suppose they're plenty fun to read for some people, of course, but it tends to eat plot alive and suffocate any character development when poorly executed).
Basically, I'm saying men are just too damn excitable and don't think about other human beings as human beings, amiright? Fite me. XD
So, yeah, this "theory" of mine is garbage and possibly got offensive and sexist somewhere along the line, but I feel like I've got my hands around some of the edges of some truth in there somewhere? ~w~ I CAN JUST FEEL IT
'kay it's bedtime now. I'm terribly sorry if you've read this far. It all sounded less stupid in my head before I typed it, I swear.