I debated the same thing when I was working on mine. After a bunch of dry-fitting and staring off into space for long periods of time, I ended up mounting the intakes first, then adding the forward fuselage.
That made it easier to deal with the intake seams, but I ended up distorting the front end of the main fuselage a bit. That affected how the forward fuselage lined up. Nothing major, but it took some work to fix the fuselage seam.
Think it's one of the those "six of one, half dozen of the other" deals. I love the Hasegawa kit, but its reputation as being "fiddly" to build is well-deserved.
Mark