Could well be slot management. If the slots over the direct route get too extreme they refile via detours, lower levels, e.t.c. These expert systems and the folks in front of them (I used to be one ages ago) know the tricks where to file in order to avoid the biggest restrictions. Obviously such massive detours are avoided in any but the most extreme cases (such as industrial action with whole sectors totally closed) but they can happen when a 2 hour slot delay can be circumnavigated with a 30 minutes detour.
The other bit would be the conditional route availability over France, which often do not allow a direct flight either.
In my time in dispatch, I’ve seen things like Switzerland – Canarias having to avoid continental Spain, London was always a game between the routes via France and Germany, sometimes we had to reroute the western Greek flights out of Italy e.t.c. Then we did it mostly manually and by experience, today there are much advanced systems in use (so I am told) which actually understand all the madness of CDR’s and Flow restriction messages by themselfs and file accordingly.
Josh wrote:
but in Spain ATC have been working to rule for several years and you fly the exact filed route, traffic or not. It adds massive overheads and is a continuous source of frustration.
I don’t know if they still do that, but they did the ‘work-to-rules’ slo-go for some time to protest some attempt by AENA (or whoever controls them) to introduce some efficiencies and lower the absurd salaries. I cannot even remember how many times I heard a CAT crew ask for a shortcut and got told ‘negative, cleared as filed’….. there were some pretty contentious exchanges of the radio!
FWIW I probably flew between London and Malaga well INXS of a 100 times and with very few exceptions the routing was always pretty direct. Malaga – Bailen VOR – Madrid – Bilbao/Santander – Vannes – Jersey – and then into the London area, depending which airport we were going to.
Their work to rule includes filed levels. If you have filed at 450 but there is a step of say 320 there as an IFPS artefact (as there are on many flight plans) you will fly capped at that level on that route no matter what time of day or night (I have seen it at 3 in the morning as well as busy times.)
Josh wrote:
If you have filed at 450 but there is a step of say 320 there as an IFPS artefact (as there are on many flight plans) you will fly capped at that level on that route no matter what time of day or night (I have seen it at 3 in the morning as well as busy times.)
That is a well known problem of the NATS software. When they import the flight plans from Eurocontrol, they only get the original altitude as given in item 15 and do not see step climbs later. When NATS ask you about the desired flight level, they do not know what you have filed and validated. Something the NATS developer got wrong in 1960 or so 
Possibly the same issue with Spain although I have not heard of it.
What does this mean, really?
Most bigger airport already use AMAN. It looks like this
This is basically a timeline with aircraft on it. The timeline represent runway occupation. It’s refreshed according to aircraft radar positions. It calculates the expected approach time (EAT) for each airrcraft. It takes wind and wake turbulence spacing into account.
With the EAT information, ACC can delay aircraft way before the IAF thus avoiding hold at low altitude.
On the above picture, you can see that runway 27R is closed for about 10 minutes.
