Ok, a concrete example.
I decide I want to go home to visit mom in Indiana, and I SPECIFICALLY want a flightplan which goes:
KLZU WOMAC HRS V51 ZORRO AZUMO KVPZ
So, I enter KLZU-KVPZ, low airways. The resulting flight plan is
WOMAC V463 HRS V267 VXV V97 CVG V517 RID V340 AZUMO
Hmmm, I want to go a different way. So I try typing the following into the flight plan section:
WOMAC HRS V51 ZORRO AZUMO
But, it does not update the chart or the route. Grrrr.
Next, I try to tell it the route using the mouse. I start out with KLZU - KVPZ Direct, and start inserting waypoints. I start with the routing tool - it has a button to delete a waypoint, but no tool to insert one. Right click for context menu? No go. Highlight the destination and press the INSERT button? Similar results.
Ok I've got a straight line between start and finish, on to the map. Right-click on WOMAC, select "Add to Route. Same for HRS, ZORRO, and AZUMO. But, no airway between HRS and ZORRO... Hmmm.
Right click on ZORRO again, select "What's here" and there is V51 as plain as the nose on my face along with a button "Add to Route." But, it is grayed out. Click on V51, double click (gives info); right click - all useless. I cannot add V51 to my route no matter what I do.
Back to the routing tools box - maybe I need to select both my entry and exit points? Select HRS then ZORRO - nothing. CTRL-select - no good. SHIFT-select - no good.
Ah, what's this? Drag and drop HRS to ZORRO - nuts, it just swaps the points.
Finally - go and add every single point along V51. Nope - it just gives a flight plan with all of those points.
So, something which is infinitely simple with paper and pencil, or with my GNS 480, is IMPOSSIBLE to do with their flight planning software. You cannot enter the flight plan in the way ATC gives it to you, which is our "natural language" as pilots.
And finally, lest you think "why would you not just accept the flight plan it gives you?" - think about how many times 50 miles variation on a long trip means the difference between sunny VFR an slogging through the ick...