The issue is not fuel burn or shorter (direct) routings is about maximizing capacity, i.e. moving a maximum of aircfaft in a given piece of airspace .
Every controller hates to be told what to to with his traffic once he/she is in charge ( that included me ) and giving a direct is what the pilot (normally) wants, save time and fuel, I get the a/c sooner away to the next frequency, everyone happy.
That was the old way.
Now let me try to explain the today way in short :
Today is max capacity to avoid delays.(*) If you want this as a goal, you start to do something like in the busy parts of the USA, everyone on fixed tracks, same speed , 5 or 10 NM appart, very, very early descents.
Today 55-60a/c per hour per sector is max. So if the less busy sectors down the route give a direct to everyone , some will get early and a sector-funnel down the line will get 65 or 70 and that becomes a safety issue.
Same reasoning with RFLs. If everyone request 350+ cruising to CFMU , you get delays, but if the mid sector 290-340 is less busy , airline X might want to refile a lower cruising level to get no delay through that area.
Pilot still like higher of course, but if the controller obliges the system no longer works.
Difficult transition times between controllers trained the old way and the maximizing capacity issues of today
As to those that believe the 2 or 3 min make no difference, revisit Ueberlingen. ATC system down, 7min on the stips, no problem. Both aircraft sent direct by previous centres, 0 min abeam TRA.
(*) This is today, might change tomorrow with oil at 150US/barell.